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. Introduction EnBio 

. Themes and Concepts of Biology EnBio 
. The Process of Science EnBio 

. The Building Blocks of Molecules EnBio 
. Water EnBio 

. Biological Molecules EnBio 

. Introduction Cells EnBio 

. How Cells Are Studied EnBio 


. Eukaryotic Cells EnBio 

. The Cell Membrane EnBio 

. Passive ‘Transport EnBio 

. Introduction Obtain Energy EnBio 

. Energy and Metabolism EnBio 

. Fermentation EnBio 

. Introduction Photosynthesis EnBio 

. Appendix EnBio 

. AIP EnBio 

. Biogeochemical Cycles EnBio 

. Biotechnology in Medicine and Agriculture EnBio 
. The Cell Cycle EnBio 

. Cloning and Genetic Engineering EnBio 
. Community Ecology EnBio 

. Discovering How Populations Change EnBio 
. DNA Replication EnBio 

. Energy Flow through Ecosystems EnBio 
. Evidence of Evolution EnBio 

. The Genome EnBio 

. How Genes Are Regulated EnBio 

. The Human Population EnBio 

. Importance of Biodiversity EnBio 


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Introduction Biotechnology EnBio 
Introduction Conservation & Biodiversity EnBio 
Introduction Ecology EnBio 

Introduction Ecosystems & Biosphere EnBio 
Introduction Evolution & Its Processes EnBio 
Introduction Molecular Biology EnBio 
Introduction Patterns Inheritance EnBio 
Introduction Reproduction 2 EnBio 
Introduction Reproduction EnBio 

Laws of Inheritance EnBio 

Mendel’s Experiments EnBio 

Photosynthesis EnBio 

Population Growth and Regulation EnBio 
The Process of Science EnBio 

Prokaryotic Cell Division EnBio 

Sexual Reproduction EnBio 

The Structure of DNA EnBio 

Threats to Biodiversity EnBio 

‘Transcription EnBio 

Translation EnBio 


Introduction EnBio 
class="introduction" 
This NASA 
image isa 
composite 
of several 
satellite- 
based views 
of Earth. To 
make the 
whole-Earth 
image, 
NASA 
scientists 
combine 
observations 
of different 
parts of the 
planet. 
(credit: 
modificatio 
n of work 
by NASA) 


Viewed from space, Earth ([link]) offers few clues about the diversity of life 
forms that reside there. The first forms of life on Earth are thought to have 
been microorganisms that existed for billions of years before plants and 
animals appeared. The mammals, birds, and flowers so familiar to us are all 
relatively recent, originating 130 to 200 million years ago. Humans have 
inhabited this planet for only the last 2.5 million years, and only in the last 
200,000 years have humans started looking like we do today. 


Themes and Concepts of Biology EnBio 
By the end of this section, you will be able to: 


e Identify and describe the properties of life 
e Describe the levels of organization among living things 
e List examples of different sub disciplines in biology 


Biology is the science that studies life. What exactly is life? This may 
sound like a silly question with an obvious answer, but it is not easy to 
define life. For example, a branch of biology called virology studies 
viruses, which exhibit some of the characteristics of living entities but lack 
others. It turns out that although viruses can attack living organisms, cause 
diseases, and even reproduce, they do not meet the criteria that biologists 
use to define life. 


From its earliest beginnings, biology has wrestled with four questions: 
What are the shared properties that make something “alive”? How do those 
various living things function? When faced with the remarkable diversity of 
life, how do we organize the different kinds of organisms so that we can 
better understand them? And, finally—what biologists ultimately seek to 
understand—how did this diversity arise and how is it continuing? As new 
organisms are discovered every day, biologists continue to seek answers to 
these and other questions. 


Properties of Life 


All groups of living organisms share several key characteristics or 
functions: order, sensitivity or response to stimuli, reproduction, adaptation, 
growth and development, regulation, homeostasis, and energy processing. 
When viewed together, these eight characteristics serve to define life. 


Order 


Organisms are highly organized structures that consist of one or more cells. 
Even very simple, single-celled organisms are remarkably complex. Inside 
each cell, atoms make up molecules. These in turn make up cell 


components or organelles. Multicellular organisms, which may consist of 
millions of individual cells, have an advantage over single-celled organisms 
in that their cells can be specialized to perform specific functions, and even 
sacrificed in certain situations for the good of the organism as a whole. How 
these specialized cells come together to form organs such as the heart, lung, 
or skin in organisms like the toad shown in [link] will be discussed later. 


A toad represents a highly 
organized structure consisting of 
cells, tissues, organs, and organ 

systems. (credit: 

"Ivengo(RUS)"/Wikimedia 

Commons) 


Sensitivity or Response to Stimuli 


Organisms respond to diverse stimuli. For example, plants can bend toward 
a source of light or respond to touch ([link]). Even tiny bacteria can move 
toward or away from chemicals (a process called chemotaxis) or light 
(phototaxis). Movement toward a stimulus is considered a positive 
response, while movement away from a stimulus is considered a negative 
response. 


The leaves of this sensitive plant 
(Mimosa pudica) will instantly 
droop and fold when touched. 
After a few minutes, the plant 

returns to its normal state. (credit: 

Alex Lomas) 


Note: 
Concept in Action 


— 
mess Openstax COLLEGE 


. 
z 


Watch this video to see how the sensitive plant responds to a touch 
stimulus. 


Reproduction 


Single-celled organisms reproduce by first duplicating their DNA, which is 
the genetic material, and then dividing it equally as the cell prepares to 
divide to form two new cells. Many multicellular organisms (those made up 
of more than one cell) produce specialized reproductive cells that will form 
new individuals. When reproduction occurs, DNA containing genes is 
passed along to an organism’s offspring. These genes are the reason that the 
offspring will belong to the same species and will have characteristics 
similar to the parent, such as fur color and blood type. 


Adaptation 


All living organisms exhibit a “fit” to their environment. Biologists refer to 
this fit as adaptation and it is a consequence of evolution by natural 
selection, which operates in every lineage of reproducing organisms. 
Examples of adaptations are diverse and unique, from heat-resistant 
Archaea that live in boiling hot springs to the tongue length of a nectar- 
feeding moth that matches the size of the flower from which it feeds. All 
adaptations enhance the reproductive potential of the individual exhibiting 
them, including their ability to survive to reproduce. Adaptations are not 
constant. As an environment changes, natural selection causes the 
characteristics of the individuals in a population to track those changes. 


Growth and Development 


Organisms grow and develop according to specific instructions coded for by 
their genes. These genes provide instructions that will direct cellular growth 
and development, ensuring that a species’ young ([link]) will grow up to 
exhibit many of the same characteristics as its parents. 


Although no two look alike, these 
kittens have inherited genes from both 
parents and share many of the same 
characteristics. (credit: Pieter & Renée 
Lanser) 


Regulation 


Even the smallest organisms are complex and require multiple regulatory 
mechanisms to coordinate internal functions, such as the transport of 
nutrients, response to stimuli, and coping with environmental stresses. For 
example, organ systems such as the digestive or circulatory systems 
perform specific functions like carrying oxygen throughout the body, 
removing wastes, delivering nutrients to every cell, and cooling the body. 


Homeostasis 


To function properly, cells require appropriate conditions such as proper 
temperature, pH, and concentrations of diverse chemicals. These conditions 
may, however, change from one moment to the next. Organisms are able to 


maintain internal conditions within a narrow range almost constantly, 
despite environmental changes, through a process called homeostasis or 
“steady state”—the ability of an organism to maintain constant internal 
conditions. For example, many organisms regulate their body temperature 
in a process known as thermoregulation. Organisms that live in cold 
climates, such as the polar bear ([link]), have body structures that help them 
withstand low temperatures and conserve body heat. In hot climates, 
organisms have methods (such as perspiration in humans or panting in 
dogs) that help them to shed excess body heat. 


Polar bears and other mammals living 
in ice-covered regions maintain their 
body temperature by generating heat 

and reducing heat loss through thick fur 
and a dense layer of fat under their 
skin. (credit: "longhorndave"/Flickr) 


Energy Processing 


All organisms (such as the California condor shown in [link]) use a source 
of energy for their metabolic activities. Some organisms capture energy 
from the Sun and convert it into chemical energy in food; others use 
chemical energy from molecules they take in. 


A lot of energy is required for 
a California condor to fly. 
Chemical energy derived 

from food is used to power 
flight. California condors are 
an endangered species; 
scientists have strived to 
place a wing tag on each bird 
to help them identify and 
locate each individual bird. 
(credit: Pacific Southwest 
Region U.S. Fish and 
Wildlife) 


Levels of Organization of Living Things 


Living things are highly organized and structured, following a hierarchy on 
a scale from small to large. The atom is the smallest and most fundamental 
unit of matter. It consists of a nucleus surrounded by electrons. Atoms form 
molecules. A molecule is a chemical structure consisting of at least two 
atoms held together by a chemical bond. Many molecules that are 
biologically important are macromolecules, large molecules that are 
typically formed by combining smaller units called monomers. An example 
of a macromolecule is deoxyribonucleic acid (DNA) ([link]), which 
contains the instructions for the functioning of the organism that contains it. 


A molecule, like this 
large DNA molecule, is 
composed of atoms. 
(credit: 
"Brian0918"/Wikimedi 
a Commons) 


Note: 
Concept in Action 


rena 
TRALEE 
TET 5 
[asia 


To see an animation of this DNA molecule, click here. 


Some cells contain aggregates of macromolecules surrounded by 
membranes; these are called organelles. Organelles are small structures that 
exist within cells and perform specialized functions. All living things are 
made of cells; the cell itself is the smallest fundamental unit of structure and 
function in living organisms. (This requirement is why viruses are not 
considered living: they are not made of cells. To make new viruses, they 
have to invade and hijack a living cell; only then can they obtain the 
materials they need to reproduce.) Some organisms consist of a single cell 
and others are multicellular. Cells are classified as prokaryotic or 
eukaryotic. Prokaryotes are single-celled organisms that lack organelles 
surrounded by a membrane and do not have nuclei surrounded by nuclear 
membranes; in contrast, the cells of eukaryotes do have membrane-bound 
organelles and nuclei. 


In most multicellular organisms, cells combine to make tissues, which are 
groups of similar cells carrying out the same function. Organs are 
collections of tissues grouped together based on a common function. 
Organs are present not only in animals but also in plants. An organ system 
is a higher level of organization that consists of functionally related organs. 
For example vertebrate animals have many organ systems, such as the 


circulatory system that transports blood throughout the body and to and 
from the lungs; it includes organs such as the heart and blood vessels. 
Organisms are individual living entities. For example, each tree in a forest 
is an organism. Single-celled prokaryotes and single-celled eukaryotes are 
also considered organisms and are typically referred to as microorganisms. 


Note: 
Art Connection 


Atom: A basic unit of matter that 
consists of a dense central nucleus 


surrounded by a cloud of negatively 
charged electrons. 


Molecule: A phospholipid, composed 
of many atoms. 


Organelles: Structures that perform 
functions within a cell. Highlighted in 
blue are a Golgi apparatus and a 

nucleus. 


Cells: Human blood cells. 


Tissue: Human skin tissue. 


Organs and organ systems: 
Organs such as the stomach and 
intestine make up part of the 

human digestive system. 


Organisms, populations, and 
communities: In a park, each person 
is an organism. Together, all the 
people make up a population. All the 
plant and animal species in the park 
comprise a community. 


Ecosystem: The ecosystem of 
Central Park in New York includes 

living organisms and the environment 
in which they live. 


The biosphere: Encompasses all 
the ecosystems on Earth. 


From an atom to the 
entire Earth, biology 
examines all aspects of 
life. (credit "molecule": 
modification of work by 


Jane Whitney; credit 
"organelles": 
modification of work by 
Louisa Howard; credit 
"cells": modification of 
work by Bruce Wetzel, 
Harry Schaefer, National 
Cancer Institute; credit 
"tissue": modification of 
work by 
"Kilbad"/Wikimedia 
Commons; credit 
"organs": modification of 
work by Mariana Ruiz 
Villareal, Joaquim Alves 
Gaspar; credit 
"organisms": 
modification of work by 
Peter Dutton; credit 
"ecosystem": 
modification of work by 
"9}914791"/Flickr; credit 
"biosphere": modification 
of work by NASA) 


Which of the following statements is false? 


a. Tissues exist within organs which exist within organ systems. 

b. Communities exist within populations which exist within ecosystems. 
c. Organelles exist within cells which exist within tissues. 

d. Communities exist within ecosystems which exist in the biosphere. 


All the individuals of a species living within a specific area are collectively 
called a population. For example, a forest may include many white pine 
trees. All of these pine trees represent the population of white pine trees in 
this forest. Different populations may live in the same specific area. For 
example, the forest with the pine trees includes populations of flowering 
plants and also insects and microbial populations. A community is the set 
of populations inhabiting a particular area. For instance, all of the trees, 
flowers, insects, and other populations in a forest form the forest’s 
community. The forest itself is an ecosystem. An ecosystem consists of all 
the living things in a particular area together with the abiotic, or non-living, 
parts of that environment such as nitrogen in the soil or rainwater. At the 
highest level of organization ({link]), the biosphere is the collection of all 
ecosystems, and it represents the zones of life on Earth. It includes land, 
water, and portions of the atmosphere. 


The Diversity of Life 


The science of biology is very broad in scope because there is a tremendous 
diversity of life on Earth. The source of this diversity is evolution, the 
process of gradual change during which new species arise from older 
species. Evolutionary biologists study the evolution of living things in 
everything from the microscopic world to ecosystems. 


In the 18th century, a scientist named Carl Linnaeus first proposed 
organizing the known species of organisms into a hierarchical taxonomy. In 
this system, species that are most similar to each other are put together 
within a grouping known as a genus. Furthermore, similar genera (the plural 
of genus) are put together within a family. This grouping continues until all 
organisms are collected together into groups at the highest level. The 
current taxonomic system now has eight levels in its hierarchy, from lowest 
to highest, they are: species, genus, family, order, class, phylum, kingdom, 
domain. Thus species are grouped within genera, genera are grouped within 
families, families are grouped within orders, and so on ({link]). 


DOMAIN 


Fox Lion Mouse Whale Fish Earthworm Paramecium 
Eukarya Sn. h 


Dog Wolt “Coyote Seal Human Bat jake Mot Tree 


KINGDOM Lion Mouse Whale Fish Earthworm 
Animalia Dog Wolf Coyote Fox "Seal Human Bat_—s Snake Moth 
PHYLUM Lion Mouse Whale Fish 

Chordata Dog met “Cote Fox Seal Human Bat Snake 

CLASS Lion Mouse Whale 

Mammalia Dog Wolf Coyote FOX Seal Human Bat 


ORDER 
Carnivora 


Lion 
Dog Wolf Coyote Fox Seal 
FAMILY 

Canine Dog Wolf Coyote Fox 
GENUS 
Came Dog Wolf Coyote 
SPECIES 


Canis lupus Dog et 


This diagram shows the levels of taxonomic hierarchy for a 
dog, from the broadest category—domain—to the most 
specific—species. 


The highest level, domain, is a relatively new addition to the system since 
the 1990s. Scientists now recognize three domains of life, the Eukarya, the 
Archaea, and the Bacteria. The domain Eukarya contains organisms that 
have cells with nuclei. It includes the kingdoms of fungi, plants, animals, 
and several kingdoms of protists. The Archaea, are single-celled organisms 
without nuclei and include many extremophiles that live in harsh 
environments like hot springs. The Bacteria are another quite different 
group of single-celled organisms without nuclei ([link]). Both the Archaea 
and the Bacteria are prokaryotes, an informal name for cells without nuclei. 
The recognition in the 1990s that certain “bacteria,” now known as the 
Archaea, were as different genetically and biochemically from other 
bacterial cells as they were from eukaryotes, motivated the recommendation 
to divide life into three domains. This dramatic change in our knowledge of 
the tree of life demonstrates that classifications are not permanent and will 
change when new information becomes available. 


In addition to the hierarchical taxonomic system, Linnaeus was the first to 
name organisms using two unique names, now called the binomial naming 
system. Before Linnaeus, the use of common names to refer to organisms 


caused confusion because there were regional differences in these common 
names. Binomial names consist of the genus name (which is capitalized) 
and the species name (all lower-case). Both names are set in italics when 
they are printed. Every species is given a unique binomial which is 
recognized the world over, so that a scientist in any location can know 
which organism is being referred to. For example, the North American blue 
jay is known uniquely as Cyanocitta cristata. Our own species is Homo 
sapiens. 


(b) 


These images represent different domains. The scanning electron 
micrograph shows (a) bacterial cells belong to the domain Bacteria, 
while the (b) extremophiles, seen all together as colored mats in this 

hot spring, belong to domain Archaea. Both the (c) sunflower and (d) 
lion are part of domain Eukarya. (credit a: modification of work by 
Rocky Mountain Laboratories, NIAID, NIH; credit b: modification of 
work by Steve Jurvetson; credit c: modification of work by Michael 
Arrighi; credit d: modification of work by Frank Vassen) 


Note: 

Evolution in Action 

Carl Woese and the Phylogenetic Tree 

The evolutionary relationships of various life forms on Earth can be 
summarized in a phylogenetic tree. A phylogenetic tree is a diagram 
showing the evolutionary relationships among biological species based on 


similarities and differences in genetic or physical traits or both. A 
phylogenetic tree is composed of branch points, or nodes, and branches. 
The internal nodes represent ancestors and are points in evolution when, 
based on scientific evidence, an ancestor is thought to have diverged to 
form two new species. The length of each branch can be considered as 
estimates of relative time. 

In the past, biologists grouped living organisms into five kingdoms: 
animals, plants, fungi, protists, and bacteria. The pioneering work of 
American microbiologist Carl Woese in the early 1970s has shown, 
however, that life on Earth has evolved along three lineages, now called 
domains—Bacteria, Archaea, and Eukarya. Woese proposed the domain as 
anew taxonomic level and Archaea as a new domain, to reflect the new 
phylogenetic tree ({link]). Many organisms belonging to the Archaea 
domain live under extreme conditions and are called extremophiles. To 
construct his tree, Woese used genetic relationships rather than similarities 
based on morphology (shape). Various genes were used in phylogenetic 
studies. Woese’s tree was constructed from comparative sequencing of the 
genes that are universally distributed, found in some slightly altered form 
in every organism, conserved (meaning that these genes have remained 
only slightly changed throughout evolution), and of an appropriate length. 


Phylogenetic Tree of Life 
, = You are here 


Bacteria Archaea Eukarya 
Green 
Filamentous Sli 
Spirochetes bacteria Entamoebae pent Animals 
Simic 
Gram Methanosarcina ame 
_ \ positives! —jyethanobacterium Halophiles 
Proteobacteria Plants 
: Methanococcus 
Cyanobacteria Ciliates 
T. celer 
Planctomyces Thermoproteus Flagellates 
Pyrodicticum 
Bacteroides Trichomonads 


Cytophaga 
Microsporidia 
Thermotoga 


Diplomonads 
Aquifex 


This phylogenetic tree was constructed by microbiologist 


Carl Woese using genetic relationships. The tree shows 
the separation of living organisms into three domains: 
Bacteria, Archaea, and Eukarya. Bacteria and Archaea 
are organisms without a nucleus or other organelles 
surrounded by a membrane and, therefore, are 
prokaryotes. (credit: modification of work by Eric Gaba) 


Branches of Biological Study 


The scope of biology is broad and therefore contains many branches and 
sub disciplines. Biologists may pursue one of those sub disciplines and 
work in a more focused field. For instance, molecular biology studies 
biological processes at the molecular level, including interactions among 
molecules such as DNA, RNA, and proteins, as well as the way they are 
regulated. Microbiology is the study of the structure and function of 
microorganisms. It is quite a broad branch itself, and depending on the 
subject of study, there are also microbial physiologists, ecologists, and 
geneticists, among others. 


Another field of biological study, neurobiology, studies the biology of the 
nervous system, and although it is considered a branch of biology, it is also 
recognized as an interdisciplinary field of study known as neuroscience. 
Because of its interdisciplinary nature, this sub discipline studies different 
functions of the nervous system using molecular, cellular, developmental, 
medical, and computational approaches. 


Researchers work on excavating 
dinosaur fossils at a site in Castellon, 
Spain. (credit: Mario Modesto) 


Paleontology, another branch of biology, uses fossils to study life’s history 
({link]). Zoology and botany are the study of animals and plants, 
respectively. Biologists can also specialize as biotechnologists, ecologists, 
or physiologists, to name just a few areas. Biotechnologists apply the 
knowledge of biology to create useful products. Ecologists study the 
interactions of organisms in their environments. Physiologists study the 
workings of cells, tissues and organs. This is just a small sample of the 
many fields that biologists can pursue. From our own bodies to the world 
we live in, discoveries in biology can affect us in very direct and important 
ways. We depend on these discoveries for our health, our food sources, and 
the benefits provided by our ecosystem. Because of this, knowledge of 
biology can benefit us in making decisions in our day-to-day lives. 


The development of technology in the twentieth century that continues 
today, particularly the technology to describe and manipulate the genetic 
material, DNA, has transformed biology. This transformation will allow 
biologists to continue to understand the history of life in greater detail, how 
the human body works, our human origins, and how humans can survive as 


a species on this planet despite the stresses caused by our increasing 
numbers. Biologists continue to decipher huge mysteries about life 
suggesting that we have only begun to understand life on the planet, its 
history, and our relationship to it. For this and other reasons, the knowledge 
of biology gained through this textbook and other printed and electronic 
media should be a benefit in whichever field you enter. 


Section Summary 


Biology is the science of life. All living organisms share several key 
properties such as order, sensitivity or response to stimuli, reproduction, 
adaptation, growth and development, regulation, homeostasis, and energy 
processing. Living things are highly organized following a hierarchy that 
includes atoms, molecules, organelles, cells, tissues, organs, and organ 
systems. Organisms, in turn, are grouped as populations, communities, 
ecosystems, and the biosphere. Evolution is the source of the tremendous 
biological diversity on Earth today. A diagram called a phylogenetic tree 
can be used to show evolutionary relationships among organisms. Biology 
is very broad and includes many branches and sub disciplines. Examples 
include molecular biology, microbiology, neurobiology, zoology, and 
botany, among others. 


Glossary 


atom 
a basic unit of matter that cannot be broken down by normal chemical 
reactions 


biology 
the study of living organisms and their interactions with one another 
and their environments 


biosphere 
a collection of all ecosystems on Earth 


cell 
the smallest fundamental unit of structure and function in living things 


community 
a set of populations inhabiting a particular area 


ecosystem 
all living things in a particular area together with the abiotic, nonliving 
parts of that environment 


eukaryote 
an organism with cells that have nuclei and membrane-bound 
organelles 


evolution 
the process of gradual change in a population that can also lead to new 
species arising from older species 


homeostasis 
the ability of an organism to maintain constant internal conditions 


macromolecule 
a large molecule typically formed by the joining of smaller molecules 


molecule 
a chemical structure consisting of at least two atoms held together by a 
chemical bond 


organ 
a structure formed of tissues operating together to perform a common 
function 


organ system 
the higher level of organization that consists of functionally related 
organs 


organelle 
a membrane-bound compartment or sac within a cell 


organism 
an individual living entity 


phylogenetic tree 
a diagram showing the evolutionary relationships among biological 
species based on similarities and differences in genetic or physical 
traits or both 


population 
all individuals within a species living within a specific area 


prokaryote 
a unicellular organism that lacks a nucleus or any other membrane- 
bound organelle 


tissue 
a group of similar cells carrying out the same function 


The Process of Science EnBio 
By the end of this section, you will be able to: 


Identify the shared characteristics of the natural sciences 
e Understand the process of scientific inquiry 

¢ Compare inductive reasoning with deductive reasoning 
e Describe the goals of basic science and applied science 


Formerly called blue-green algae, the (a) cyanobacteria 
seen through a light microscope are some of Earth’s 
oldest life forms. These (b) stromatolites along the 
shores of Lake Thetis in Western Australia are ancient 
structures formed by the layering of cyanobacteria in 
shallow waters. (credit a: modification of work by 
NASA; scale-bar data from Matt Russell; credit b: 
modification of work by Ruth Ellison) 


Like geology, physics, and chemistry, biology is a science that gathers 
knowledge about the natural world. Specifically, biology is the study of life. 
The discoveries of biology are made by a community of researchers who 
work individually and together using agreed-on methods. In this sense, 
biology, like all sciences is a social enterprise like politics or the arts. The 
methods of science include careful observation, record keeping, logical and 
mathematical reasoning, experimentation, and submitting conclusions to the 
scrutiny of others. Science also requires considerable imagination and 


creativity; a well-designed experiment is commonly described as elegant, or 
beautiful. Like politics, science has considerable practical implications and 
some science is dedicated to practical applications, such as the prevention 
of disease (see [link]). Other science proceeds largely motivated by 
curiosity. Whatever its goal, there is no doubt that science, including 
biology, has transformed human existence and will continue to do so. 


Biologists may choose to study Escherichia 
coli (E. coli), a bacterium that is a normal 
resident of our digestive tracts but which is 
also sometimes responsible for disease 
outbreaks. In this micrograph, the bacterium 
is visualized using a scanning electron 
microscope and digital colorization. (credit: 
Eric Erbe; digital colorization by 
Christopher Pooley, USDA-ARS) 


The Nature of Science 


Biology is a science, but what exactly is science? What does the study of 
biology share with other scientific disciplines? Science (from the Latin 


scientia, meaning "knowledge") can be defined as knowledge about the 
natural world. 


Science is a very specific way of learning, or knowing, about the world. 
The history of the past 500 years demonstrates that science is a very 
powerful way of knowing about the world; it is largely responsible for the 
technological revolutions that have taken place during this time. There are 
however, areas of knowledge and human experience that the methods of 
science cannot be applied to. These include such things as answering purely 
moral questions, aesthetic questions, or what can be generally categorized 
as spiritual questions. Science has cannot investigate these areas because 
they are outside the realm of material phenomena, the phenomena of matter 
and energy, and cannot be observed and measured. 


The scientific method is a method of research with defined steps that 
include experiments and careful observation. The steps of the scientific 
method will be examined in detail later, but one of the most important 
aspects of this method is the testing of hypotheses. A hypothesis is a 
suggested explanation for an event, which can be tested. Hypotheses, or 
tentative explanations, are generally produced within the context of a 
scientific theory. A scientific theory is a generally accepted, thoroughly 
tested and confirmed explanation for a set of observations or phenomena. 
Scientific theory is the foundation of scientific knowledge. In addition, in 
many scientific disciplines (less so in biology) there are scientific laws, 
often expressed in mathematical formulas, which describe how elements of 
nature will behave under certain specific conditions. There is not an 
evolution of hypotheses through theories to laws as if they represented 
some increase in certainty about the world. Hypotheses are the day-to-day 
material that scientists work with and they are developed within the context 
of theories. Laws are concise descriptions of parts of the world that are 
amenable to formulaic or mathematical description. 


Natural Sciences 


What would you expect to see in a museum of natural sciences? Frogs? 
Plants? Dinosaur skeletons? Exhibits about how the brain functions? A 


planetarium? Gems and minerals? Or maybe all of the above? Science 
includes such diverse fields as astronomy, biology, computer sciences, 
geology, logic, physics, chemistry, and mathematics ([link]). However, 
those fields of science related to the physical world and its phenomena and 
processes are considered natural sciences. Thus, a museum of natural 
sciences might contain any of the items listed above. 


Some fields of science include 
astronomy, biology, computer 
science, geology, logic, physics, 
chemistry, and mathematics. 
(credit: "Image Editor"/Flickr) 


There is no complete agreement when it comes to defining what the natural 
sciences include. For some experts, the natural sciences are astronomy, 
biology, chemistry, earth science, and physics. Other scholars choose to 
divide natural sciences into life sciences, which study living things and 
include biology, and physical sciences, which study nonliving matter and 


include astronomy, physics, and chemistry. Some disciplines such as 
biophysics and biochemistry build on two sciences and are interdisciplinary. 


Scientific Inquiry 


One thing is common to all forms of science: an ultimate goal “to know.” 
Curiosity and inquiry are the driving forces for the development of science. 
Scientists seek to understand the world and the way it operates. Two 
methods of logical thinking are used: inductive reasoning and deductive 
reasoning. 


Inductive reasoning is a form of logical thinking that uses related 
observations to arrive at a general conclusion. This type of reasoning is 
common in descriptive science. A life scientist such as a biologist makes 
observations and records them. These data can be qualitative (descriptive) 
or quantitative (consisting of numbers), and the raw data can be 
supplemented with drawings, pictures, photos, or videos. From many 
observations, the scientist can infer conclusions (inductions) based on 
evidence. Inductive reasoning involves formulating generalizations inferred 
from careful observation and the analysis of a large amount of data. Brain 
studies often work this way. Many brains are observed while people are 
doing a task. The part of the brain that lights up, indicating activity, is then 
demonstrated to be the part controlling the response to that task. 


Deductive reasoning or deduction is the type of logic used in hypothesis- 
based science. In deductive reasoning, the pattern of thinking moves in the 
opposite direction as compared to inductive reasoning. Deductive 
reasoning is a form of logical thinking that uses a general principle or law 
to forecast specific results. From those general principles, a scientist can 
extrapolate and predict the specific results that would be valid as long as the 
general principles are valid. For example, a prediction would be that if the 
climate is becoming warmer in a region, the distribution of plants and 
animals should change. Comparisons have been made between distributions 
in the past and the present, and the many changes that have been found are 
consistent with a warming climate. Finding the change in distribution is 
evidence that the climate change conclusion is a valid one. 


Both types of logical thinking are related to the two main pathways of 
scientific study: descriptive science and hypothesis-based science. 
Descriptive (or discovery) science aims to observe, explore, and discover, 
while hypothesis-based science begins with a specific question or problem 
and a potential answer or solution that can be tested. The boundary between 
these two forms of study is often blurred, because most scientific endeavors 
combine both approaches. Observations lead to questions, questions lead to 
forming a hypothesis as a possible answer to those questions, and then the 
hypothesis is tested. Thus, descriptive science and hypothesis-based science 
are in continuous dialogue. 


Hypothesis Testing 


Biologists study the living world by posing questions about it and seeking 
science-based responses. This approach is common to other sciences as well 
and is often referred to as the scientific method. The scientific method was 
used even in ancient times, but it was first documented by England’s Sir 
Francis Bacon (1561-1626) ({link]), who set up inductive methods for 
scientific inquiry. The scientific method is not exclusively used by 
biologists but can be applied to almost anything as a logical problem- 
solving method. 


Sir Francis Bacon 
is credited with 
being the first to 
document the 
scientific method. 


The scientific process typically starts with an observation (often a problem 
to be solved) that leads to a question. Let’s think about a simple problem 
that starts with an observation and apply the scientific method to solve the 
problem. One Monday morning, a student arrives at class and quickly 
discovers that the classroom is too warm. That is an observation that also 
describes a problem: the classroom is too warm. The student then asks a 
question: “Why is the classroom so warm?” 


Recall that a hypothesis is a suggested explanation that can be tested. To 
solve a problem, several hypotheses may be proposed. For example, one 
hypothesis might be, “The classroom is warm because no one turned on the 
air conditioning.” But there could be other responses to the question, and 
therefore other hypotheses may be proposed. A second hypothesis might be, 


“The classroom is warm because there is a power failure, and so the air 
conditioning doesn’t work.” 


Once a hypothesis has been selected, a prediction may be made. A 
prediction is similar to a hypothesis but it typically has the format “If... 
then ....” For example, the prediction for the first hypothesis might be, “If 
the student turns on the air conditioning, then the classroom will no longer 
be too warm.” 


A hypothesis must be testable to ensure that it is valid. For example, a 
hypothesis that depends on what a bear thinks is not testable, because it can 
never be known what a bear thinks. It should also be falsifiable, meaning 
that it can be disproven by experimental results. An example of an 
unfalsifiable hypothesis is “Botticelli’s Birth of Venus is beautiful.” There is 
no experiment that might show this statement to be false. To test a 
hypothesis, a researcher will conduct one or more experiments designed to 
eliminate one or more of the hypotheses. This is important. A hypothesis 
can be disproven, or eliminated, but it can never be proven. Science does 
not deal in proofs like mathematics. If an experiment fails to disprove a 
hypothesis, then we find support for that explanation, but this is not to say 
that down the road a better explanation will not be found, or a more 
carefully designed experiment will be found to falsify the hypothesis. 


Each experiment will have one or more variables and one or more controls. 
A variable is any part of the experiment that can vary or change during the 
experiment. A control is a part of the experiment that does not change. 
Look for the variables and controls in the example that follows. As a simple 
example, an experiment might be conducted to test the hypothesis that 
phosphate limits the growth of algae in freshwater ponds. A series of 
artificial ponds are filled with water and half of them are treated by adding 
phosphate each week, while the other half are treated by adding a salt that is 
known not to be used by algae. The variable here is the phosphate (or lack 
of phosphate), the experimental or treatment cases are the ponds with added 
phosphate and the control ponds are those with something inert added, such 
as the salt. Just adding something is also a control against the possibility 
that adding extra matter to the pond has an effect. If the treated ponds show 
lesser growth of algae, then we have found support for our hypothesis. If 


they do not, then we reject our hypothesis. Be aware that rejecting one 
hypothesis does not determine whether or not the other hypotheses can be 
accepted; it simply eliminates one hypothesis that is not valid ({link]). 
Using the scientific method, the hypotheses that are inconsistent with 
experimental data are rejected. 


Note: 
Art Connection 


Make an observation 
Ask a question 


Form a hypothesis that 
answers the question 


Make a prediction based 
on the hypothesis 


Do an experiment 


to test the prediction 


Analyze the results 


Hypothesis is 
SUPPORTED 


Report results 


The scientific method is a series 
of defined steps that include 
experiments and careful 
observation. If a hypothesis is 


Hypothesis is 
NOT SUPPORTED 


not supported by data, a new 
hypothesis can be proposed. 


In the example below, the scientific method is used to solve an everyday 
problem. Which part in the example below is the hypothesis? Which is the 
prediction? Based on the results of the experiment, is the hypothesis 
supported? If it is not supported, propose some alternative hypotheses. 


1. My toaster doesn’t toast my bread. 

2. Why doesn’t my toaster work? 

3. There is something wrong with the electrical outlet. 

4. If something is wrong with the outlet, my coffeemaker also won’t 
work when plugged into it. 

5. I plug my coffeemaker into the outlet. 

6. My coffeemaker works. 


In practice, the scientific method is not as rigid and structured as it might at 
first appear. Sometimes an experiment leads to conclusions that favor a 
change in approach; often, an experiment brings entirely new scientific 
questions to the puzzle. Many times, science does not operate in a linear 
fashion; instead, scientists continually draw inferences and make 
generalizations, finding patterns as their research proceeds. Scientific 
reasoning is more complex than the scientific method alone suggests. 


Basic and Applied Science 


The scientific community has been debating for the last few decades about 
the value of different types of science. Is it valuable to pursue science for 
the sake of simply gaining knowledge, or does scientific knowledge only 
have worth if we can apply it to solving a specific problem or bettering our 
lives? This question focuses on the differences between two types of 
science: basic science and applied science. 


Basic science or “pure” science seeks to expand knowledge regardless of 
the short-term application of that knowledge. It is not focused on 


developing a product or a service of immediate public or commercial value. 
The immediate goal of basic science is knowledge for knowledge’s sake, 
though this does not mean that in the end it may not result in an application. 


In contrast, applied science or “technology,” aims to use science to solve 
real-world problems, making it possible, for example, to improve a crop 
yield, find a cure for a particular disease, or save animals threatened by a 
natural disaster. In applied science, the problem is usually defined for the 
researcher. 


Some individuals may perceive applied science as “useful” and basic 
science as “useless.” A question these people might pose to a scientist 
advocating knowledge acquisition would be, “What for?” A careful look at 
the history of science, however, reveals that basic knowledge has resulted in 
many remarkable applications of great value. Many scientists think that a 
basic understanding of science is necessary before an application is 
developed; therefore, applied science relies on the results generated through 
basic science. Other scientists think that it is time to move on from basic 
science and instead to find solutions to actual problems. Both approaches 
are valid. It is true that there are problems that demand immediate attention; 
however, few solutions would be found without the help of the knowledge 
generated through basic science. 


One example of how basic and applied science can work together to solve 
practical problems occurred after the discovery of DNA structure led to an 
understanding of the molecular mechanisms governing DNA replication. 
Strands of DNA, unique in every human, are found in our cells, where they 
provide the instructions necessary for life. During DNA replication, new 
copies of DNA are made, shortly before a cell divides to form new cells. 
Understanding the mechanisms of DNA replication enabled scientists to 
develop laboratory techniques that are now used to identify genetic 
diseases, pinpoint individuals who were at a crime scene, and determine 
paternity. Without basic science, it is unlikely that applied science would 
exist. 


Another example of the link between basic and applied research is the 
Human Genome Project, a study in which each human chromosome was 
analyzed and mapped to determine the precise sequence of DNA subunits 


and the exact location of each gene. (The gene is the basic unit of heredity; 
an individual’s complete collection of genes is his or her genome.) Other 
organisms have also been studied as part of this project to gain a better 
understanding of human chromosomes. The Human Genome Project 
({link]) relied on basic research carried out with non-human organisms and, 
later, with the human genome. An important end goal eventually became 
using the data for applied research seeking cures for genetically related 
diseases. 


The Human Genome 


Project was a 13-year 
collaborative effort 
among researchers 
working in several 

different fields of science. 
The project was 
completed in 2003. 
(credit: the U.S. 

Department of Energy 

Genome Programs) 


While research efforts in both basic science and applied science are usually 
carefully planned, it is important to note that some discoveries are made by 
serendipity, that is, by means of a fortunate accident or a lucky surprise. 
Penicillin was discovered when biologist Alexander Fleming accidentally 
left a petri dish of Staphylococcus bacteria open. An unwanted mold grew, 
killing the bacteria. The mold turned out to be Penicillium, and a new 
antibiotic was discovered. Even in the highly organized world of science, 
luck—when combined with an observant, curious mind—can lead to 
unexpected breakthroughs. 


Reporting Scientific Work 


Whether scientific research is basic science or applied science, scientists 
must share their findings for other researchers to expand and build upon 
their discoveries. Communication and collaboration within and between sub 
disciplines of science are key to the advancement of knowledge in science. 
For this reason, an important aspect of a scientist’s work is disseminating 
results and communicating with peers. Scientists can share results by 
presenting them at a scientific meeting or conference, but this approach can 
reach only the limited few who are present. Instead, most scientists present 
their results in peer-reviewed articles that are published in scientific 
journals. Peer-reviewed articles are scientific papers that are reviewed, 
usually anonymously by a scientist’s colleagues, or peers. These colleagues 
are qualified individuals, often experts in the same research area, who judge 
whether or not the scientist’s work is suitable for publication. The process 
of peer review helps to ensure that the research described in a scientific 
paper or grant proposal is original, significant, logical, and thorough. Grant 
proposals, which are requests for research funding, are also subject to peer 
review. Scientists publish their work so other scientists can reproduce their 
experiments under similar or different conditions to expand on the findings. 
The experimental results must be consistent with the findings of other 
scientists. 


There are many journals and the popular press that do not use a peer-review 
system. A large number of online open-access journals, journals with 
articles available without cost, are now available many of which use 
rigorous peer-review systems, but some of which do not. Results of any 


studies published in these forums without peer review are not reliable and 
should not form the basis for other scientific work. In one exception, 
journals may allow a researcher to cite a personal communication from 
another researcher about unpublished results with the cited author’s 
permission. 


Section Summary 


Biology is the science that studies living organisms and their interactions 
with one another and their environments. Science attempts to describe and 
understand the nature of the universe in whole or in part. Science has many 
fields; those fields related to the physical world and its phenomena are 
considered natural sciences. 


A hypothesis is a tentative explanation for an observation. A scientific 
theory is a well-tested and consistently verified explanation for a set of 
observations or phenomena. A scientific law is a description, often in the 
form of a mathematical formula, of the behavior of an aspect of nature 
under certain circumstances. Two types of logical reasoning are used in 
science. Inductive reasoning uses results to produce general scientific 
principles. Deductive reasoning is a form of logical thinking that predicts 
results by applying general principles. The common thread throughout 
scientific research is the use of the scientific method. Scientists present their 
results in peer-reviewed scientific papers published in scientific journals. 


Science can be basic or applied. The main goal of basic science is to expand 
knowledge without any expectation of short-term practical application of 


that knowledge. The primary goal of applied research, however, is to solve 
practical problems. 


Art Connections 


Exercise: 


Problem: 


[link] In the example below, the scientific method is used to solve an 
everyday problem. Which part in the example below is the hypothesis? 
Which is the prediction? Based on the results of the experiment, is the 
hypothesis supported? If it is not supported, propose some alternative 
hypotheses. 


1. My toaster doesn’t toast my bread. 

2. Why doesn’t my toaster work? 

3. There is something wrong with the electrical outlet. 

4. If something is wrong with the outlet, my coffeemaker also won’t 
work when plugged into it. 

5. I plug my coffeemaker into the outlet. 

6. My coffeemaker works. 


Solution: 


[link] The hypothesis is #3 (there is something wrong with the 
electrical outlet), and the prediction is #4 (if something is wrong with 
the outlet, then the coffeemaker also won’t work when plugged into 
the outlet). The original hypothesis is not supported, as the coffee 
maker works when plugged into the outlet. Alternative hypotheses 
may include (1) the toaster might be broken or (2) the toaster wasn’t 
turned on. 


Multiple Choice 


Exercise: 


Problem: 


A suggested and testable explanation for an event is called a 


a. hypothesis 


b. variable 
c. theory 
d. control 


Solution: 


A 
Exercise: 


Problem: 


The type of logical thinking that uses related observations to arrive at a 
general conclusion is called 


a. deductive reasoning 

b. the scientific method 

c. hypothesis-based science 
d. inductive reasoning 


Solution: 


D 


Free Response 


Exercise: 


Problem: 


Give an example of how applied science has had a direct effect on 
your daily life. 


Solution: 


Answers will vary. One example of how applied science has had a 
direct effect on daily life is the presence of vaccines. Vaccines to 


prevent diseases such polio, measles, tetanus, and even the influenza 
affect daily life by contributing to individual and societal health. 


Glossary 


applied science 
a form of science that solves real-world problems 


basic science 
science that seeks to expand knowledge regardless of the short-term 
application of that knowledge 


control 
a part of an experiment that does not change during the experiment 


deductive reasoning 
a form of logical thinking that uses a general statement to forecast 
specific results 


descriptive science 
a form of science that aims to observe, explore, and find things out 


falsifiable 
able to be disproven by experimental results 


hypothesis 
a suggested explanation for an event, which can be tested 


hypothesis-based science 
a form of science that begins with a specific explanation that is then 
tested 


inductive reasoning 
a form of logical thinking that uses related observations to arrive at a 
general conclusion 


life science 


a field of science, such as biology, that studies living things 


natural science 
a field of science that studies the physical world, its phenomena, and 
processes 


peer-reviewed article 
a scientific report that is reviewed by a scientist’s colleagues before 
publication 


physical science 
a field of science, such as astronomy, physics, and chemistry, that 
studies nonliving matter 


science 
knowledge that covers general truths or the operation of general laws, 
especially when acquired and tested by the scientific method 


scientific law 
a description, often in the form of a mathematical formula, for the 
behavior of some aspect of nature under certain specific conditions 


scientific method 
a method of research with defined steps that include experiments and 
careful observation 


scientific theory 
a thoroughly tested and confirmed explanation for observations or 
phenomena 


variable 
a part of an experiment that can vary or change 


The Building Blocks of Molecules EnBio 


At its most fundamental level, life is made up of matter. Matter occupies 
space and has mass. All matter is composed of elements, substances that 
cannot be broken down or transformed chemically into other substances. 

Each element is made of one type of atoms. 


Each element is designated by its chemical symbol (such as H, N, O, C, and 
Na), and possesses unique properties. These unique properties allow 
elements to combine and to bond with each other in specific ways. 


Atoms 


An atom is the smallest component of an element that retains all of the 
chemical properties of that element. For example, one hydrogen atom has 
all of the properties of the element hydrogen, such as it exists as a gas at 
room temperature, and it bonds with oxygen to create a water molecule. 
Hydrogen atoms cannot be broken down into anything smaller while still 
retaining the properties of hydrogen. If a hydrogen atom were broken down 
into subatomic particles, it would no longer have the properties of 
hydrogen. 


At the most basic level, all organisms are made of a combination of 
elements. They contain atoms that combine together to form molecules. In 
multicellular organisms, such as animals, molecules can interact to form 
cells that combine to form tissues, which make up organs. These 
combinations continue until entire multicellular organisms are formed. 


Note: 
Art Connection 


Periodic Table of the Elements 18 


13 14 15 16 17 
a 


at [ 
: im u mn 


[| Other non-metals |_| Noble gases 
Number ; : 
Symbol [_] Alkali metals {| Lanthanides 
1.01 Relative |_| Transition metals [_] Actinides 
Name Hydrogen Atomic Mass [DJ Other metals [_] Unknown 


[_] Alkaline earth metals chemical 


properties 


|_| Halogens 


Arranged in columns and rows based on the characteristics of 
the elements, the periodic table provides key information about 
the elements and how they might interact with each other to 
form molecules. Most periodic tables provide a key or legend 
to the information they contain. 


There are two types of bonds that hold atoms together; polar and non-polar. 
Non-polar bonds form non-polar molecules with no charge on them, like 
carbon with carbon or carbon with hydrogen. Polar bonds form polar 
molecules with a partial charge, either positive or negative. 


Polar covalent bond Nonpolar covalent bond Nonpolar covalent double bond 


OO 


5+ 5+ 


Ce) 
On” Oo 
) 


=— Single bond 
= Double bond 


The water molecule (left) depicts a polar bond with a 
slightly positive charge on the hydrogen atoms and a 
slightly negative charge on the oxygen. Examples of 
nonpolar bonds include methane (middle) and oxygen 


(right). 


Hydrogen Bonds 


Covalent bond 


Hydrogen bond 


Hydrogen bonds form between 
slightly positive (6+) and slightly 
negative (6—) charges of polar 
covalent molecules, such as water. 


Hydrogen bonds can form between different molecules and they do not 
always have to include a water molecule. Hydrogen atoms in polar bonds 
within any molecule can form bonds with other adjacent molecules. For 
example, hydrogen bonds hold together two long strands of DNA to give 
the DNA molecule its characteristic double-stranded structure. Hydrogen 
bonds are also responsible for some of the three-dimensional structure of 
proteins. 


Section Summary 


Matter is anything that occupies space and has mass. It is made up of atoms 
of different elements. All of the 92 elements that occur naturally have 
unique qualities that allow them to combine in various ways to create 
compounds or molecules. Atoms, which consist of protons, neutrons, and 
electrons, are the smallest units of an element that retain all of the 
properties of that element. 


Glossary 


anion 
a negative ion formed by gaining electrons 


atomic number 
the number of protons in an atom 


cation 
a positive ion formed by losing electrons 


chemical bond 
an interaction between two or more of the same or different elements 
that results in the formation of molecules 


covalent bond 
a type of strong bond between two or more of the same or different 
elements; forms when electrons are shared between elements 


electron 
a negatively charged particle that resides outside of the nucleus in the 
electron orbital; lacks functional mass and has a charge of —1 


electron transfer 
the movement of electrons from one element to another 


element 
one of 118 unique substances that cannot be broken down into smaller 
substances and retain the characteristic of that substance; each element 
has a specified number of protons and unique properties 


hydrogen bond 
a weak bond between partially positively charged hydrogen atoms and 
partially negatively charged elements or molecules 


ion 
an atom or compound that does not contain equal numbers of protons 
and electrons, and therefore has a net charge 


ionic bond 
a chemical bond that forms between ions of opposite charges 


isotope 
one or more forms of an element that have different numbers of 
neutrons 


mass number 
the number of protons plus neutrons in an atom 


matter 
anything that has mass and occupies space 


neutron 
a particle with no charge that resides in the nucleus of an atom; has a 
mass of 1 


nonpolar covalent bond 


a type of covalent bond that forms between atoms when electrons are 
shared equally between atoms, resulting in no regions with partial 
charges as in polar covalent bonds 


nucleus 
(chemistry) the dense center of an atom made up of protons and 
(except in the case of a hydrogen atom) neutrons 


octet rule 
states that the outermost shell of an element with a low atomic number 
can hold eight electrons 


periodic table of elements 
an organizational chart of elements, indicating the atomic number and 
mass number of each element; also provides key information about the 
properties of elements 


polar covalent bond 
a type of covalent bond in which electrons are pulled toward one atom 
and away from another, resulting in slightly positive and slightly 
negative charged regions of the molecule 


proton 
a positively charged particle that resides in the nucleus of an atom; has 
a mass of 1 and a charge of +1 


radioactive isotope 
an isotope that spontaneously emits particles or energy to form a more 
stable element 


van der Waals interaction 
a weak attraction or interaction between molecules caused by slightly 
positively charged or slightly negatively charged atoms 


Water EnBio 
By the end of this section, you will be able to: 


e Describe the properties of water that are critical to maintaining life 


Do you ever wonder why scientists spend time looking for water on other 
planets? It is because water is essential to life; even minute traces of it on 
another planet can indicate that life could or did exist on that planet. Water 
is one of the more abundant molecules in living cells and the one most 
critical to life as we know it. Approximately 60-70 percent of your body is 
made up of water. Without it, life simply would not exist. 


Water Is Polar 


The hydrogen and oxygen atoms within water molecules form polar 
covalent bonds. The shared electrons spend more time associated with the 
oxygen atom than they do with hydrogen atoms. There is no overall charge 
to a water molecule, but there is a slight positive charge on each hydrogen 
atom and a slight negative charge on the oxygen atom. Because of these 
charges, the slightly positive hydrogen atoms repel each other and form the 
unique shape seen in [link]. Each water molecule attracts other water 
molecules because of the positive and negative charges in the different parts 
of the molecule. Water also attracts other polar molecules (such as sugars), 
forming hydrogen bonds. When a substance readily forms hydrogen bonds 
with water, it can dissolve in water and is referred to as hydrophilic 
(“water-loving”). Hydrogen bonds are not readily formed with nonpolar 
substances like oils and fats ([link]). These nonpolar compounds are 
hydrophobic (“water-fearing”) and will not dissolve in water. 


As this macroscopic image of 
oil and water show, oil is a 
nonpolar compound and, 
hence, will not dissolve in 
water. Oil and water do not 
mix. (credit: Gautam Dogra) 


Water Stabilizes Temperature 


The hydrogen bonds in water allow it to absorb and release heat energy 
more slowly than many other substances. Temperature is a measure of the 
motion (kinetic energy) of molecules. As the motion increases, energy is 
higher and thus temperature is higher. Water absorbs a great deal of energy 
before its temperature rises. Increased energy disrupts the hydrogen bonds 
between water molecules. Because these bonds can be created and disrupted 
rapidly, water absorbs an increase in energy and temperature changes only 
minimally. This means that water moderates temperature changes within 
organisms and in their environments. As energy input continues, the 
balance between hydrogen-bond formation and destruction swings toward 
the destruction side. More bonds are broken than are formed. This process 
results in the release of individual water molecules at the surface of the 
liquid (such as a body of water, the leaves of a plant, or the skin of an 
organism) in a process called evaporation. Evaporation of sweat, which is 


90 percent water, allows for cooling of an organism, because breaking 
hydrogen bonds requires an input of energy and takes heat away from the 
body. 


Conversely, as molecular motion decreases and temperatures drop, less 
energy is present to break the hydrogen bonds between water molecules. 
These bonds remain intact and begin to form a rigid, lattice-like structure 
(e.g., ice) ({link]a). When frozen, ice is less dense than liquid water (the 
molecules are farther apart). This means that ice floats on the surface of a 
body of water ({link]b). In lakes, ponds, and oceans, ice will form on the 
surface of the water, creating an insulating barrier to protect the animal and 
plant life beneath from freezing in the water. If this did not happen, plants 
and animals living in water would freeze in a block of ice and could not 
move freely, making life in cold temperatures difficult or impossible. 


(a) The lattice structure of ice makes it less dense than 
the freely flowing molecules of liquid water. Ice's lower 
density enables it to (b) float on water. (credit a: 
modification of work by Jane Whitney; credit b: 
modification of work by Carlos Ponte) 


Note: 
Concepts in Action 


[=] 
Be 


WE 


openstax COLLEGE 
: “1 
‘7b 1 
ake ae 


Click here to see a 3-D animation of the structure of an ice lattice. (credit: 
image created by Jane Whitney using Visual Molecular Dynamics (VMD) 
SOleyare ome 

Humphrey, W., Dalke, A. and Schulten, K., ""VMD—Visual Molecular 
Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. 
http://www.ks.uiuc.edu/Research/vmd/ 


Water Is an Excellent Solvent 


Because water is polar, with slight positive and negative charges, ionic 
compounds and polar molecules can readily dissolve in it. Water is, 
therefore, what is referred to as a solvent—a substance capable of 
dissolving another substance. The charged particles will form hydrogen 
bonds with a surrounding layer of water molecules. This is referred to as a 
sphere of hydration and serves to keep the particles separated or dispersed 
in the water. In the case of table salt (NaCl) mixed in water ((link]), the 
sodium and chloride ions separate, or dissociate, in the water, and spheres 
of hydration are formed around the ions. A positively charged sodium ion is 
surrounded by the partially negative charges of oxygen atoms in water 
molecules. A negatively charged chloride ion is surrounded by the partially 
positive charges of hydrogen atoms in water molecules. These spheres of 
hydration are also referred to as hydration shells. The polarity of the water 
molecule makes it an effective solvent and is important in its many roles in 
living systems. 


A single water molecule 
with partial charges 


3- 


When table salt (NaCl) is mixed in water, spheres 
of hydration form around the ions. 


Water Is Cohesive 


Have you ever filled up a glass of water to the very top and then slowly 
added a few more drops? Before it overflows, the water actually forms a 
dome-like shape above the rim of the glass. This water can stay above the 
glass because of the property of cohesion. In cohesion, water molecules are 
attracted to each other (because of hydrogen bonding), keeping the 
molecules together at the liquid-air (gas) interface, although there is no 
more room in the glass. Cohesion gives rise to surface tension, the capacity 
of a substance to withstand rupture when placed under tension or stress. 
When you drop a small scrap of paper onto a droplet of water, the paper 
floats on top of the water droplet, although the object is denser (heavier) 
than the water. This occurs because of the surface tension that is created by 
the water molecules. Cohesion and surface tension keep the water 
molecules intact and the item floating on the top. It is even possible to 


“float” a steel needle on top of a glass of water if you place it gently, 
without breaking the surface tension ((Link]). 


The weight of a needle on top of 
water pulls the surface tension 
downward; at the same time, the 
surface tension of the water is 
pulling it up, suspending the needle 
on the surface of the water and 
keeping it from sinking. Notice the 
indentation in the water around the 
needle. (credit: Cory Zanker) 


These cohesive forces are also related to the water’s property of adhesion, 
or the attraction between water molecules and other molecules. This is 
observed when water “climbs” up a straw placed in a glass of water. You 
will notice that the water appears to be higher on the sides of the straw than 
in the middle. This is because the water molecules are attracted to the straw 
and therefore adhere to it. 


Cohesive and adhesive forces are important for sustaining life. For 
example, because of these forces, water can flow up from the roots to the 
tops of plants to feed the plant. 


Note: 
Concept in Action 


pies 
. 
mss’ OPENStax COLLEGE 


To learn more about water, visit the U.S. Geological Survey Water Science 
for Schools: All About Water! website. 


Buffers, pH, Acids, and Bases 


The pH of a solution is a measure of its acidity or alkalinity. You have 
probably used litmus paper, paper that has been treated with a natural 
water-soluble dye so it can be used as a pH indicator, to test how much acid 
or base (alkalinity) exists in a solution. You might have even used some to 
make sure the water in an outdoor swimming pool is properly treated. In 
both cases, this pH test measures the amount of hydrogen ions that exists in 
a given solution. High concentrations of hydrogen ions yield a low pH, 
whereas low levels of hydrogen ions result in a high pH. The overall 
concentration of hydrogen ions is inversely related to its pH and can be 
measured on the pH scale ((link]). Therefore, the more hydrogen ions 
present, the lower the pH; conversely, the fewer hydrogen ions, the higher 
the pH. 


13 Bleach 


12 Soapy water 
11 Ammonia solution 
10 Milk of magnesia 
9 Baking soda 
8 Seawater 
7 Distilled water 
6 Urine 
5 Black coffee 
4 Tomato juice 
3 Orange juice 
2 Lemon juice 
1 Gastric acid 


The pH scale measures the amount 
of hydrogen ions (H*) ina 
substance. (credit: modification of 
work by Edward Stevens) 


Acids are substances that provide hydrogen ions (H*) and lower pH, 
whereas bases provide hydroxide ions (OH _) and raise pH. 


Section Summary 


Water has many properties that are critical to maintaining life. It is polar, 
allowing for the formation of hydrogen bonds, which allow ions and other 
polar molecules to dissolve in water. Therefore, water is an excellent 
solvent. The hydrogen bonds between water molecules give water the 
ability to hold heat better than many other substances. As the temperature 
rises, the hydrogen bonds between water continually break and reform, 
allowing for the overall temperature to remain stable, although increased 


energy is added to the system. Water’s cohesive forces allow for the 
property of surface tension. All of these unique properties of water are 
important in the chemistry of living organisms. 


The pH of a solution is a measure of the concentration of hydrogen ions in 
the solution. A solution with a high number of hydrogen ions is acidic and 
has a low pH value. A solution with a high number of hydroxide ions is 
basic and has a high pH value. The pH scale ranges from 0 to 14, with a pH 
of 7 being neutral. Buffers are solutions that moderate pH changes when an 
acid or base is added to the buffer system. Buffers are important in 
biological systems because of their ability to maintain constant pH 
conditions. 


Glossary 


acid 
a substance that donates hydrogen ions and therefore lowers pH 


adhesion 
the attraction between water molecules and molecules of a different 
substance 


base 
a substance that absorbs hydrogen ions and therefore raises pH 


buffer 
a solution that resists a change in pH by absorbing or releasing 
hydrogen or hydroxide ions 


cohesion 
the intermolecular forces between water molecules caused by the polar 
nature of water; creates surface tension 


evaporation 
the release of water molecules from liquid water to form water vapor 


hydrophilic 
describes a substance that dissolves in water; water-loving 


hydrophobic 
describes a substance that does not dissolve in water; water-fearing 


litmus paper 
filter paper that has been treated with a natural water-soluble dye so it 
can be used as a pH indicator 


PH scale 
a scale ranging from 0 to 14 that measures the approximate 
concentration of hydrogen ions of a substance 


solvent 
a substance capable of dissolving another substance 


surface tension 
the cohesive force at the surface of a body of liquid that prevents the 
molecules from separating 


temperature 
a measure of molecular motion 


Biological Molecules EnBio 
By the end of this section, you will be able to: 


e Describe the ways in which carbon is critical to life 

e Explain the impact of slight changes in amino acids on organisms 
¢ Describe the four major types of biological molecules 

e Understand the functions of the four major types of molecules 


The large molecules necessary for life that are built from smaller organic 
molecules are called biological macromolecules. There are four major 
classes of biological macromolecules (carbohydrates, lipids, proteins, and 
nucleic acids), and each is an important component of the cell and performs 
a wide array of functions. Combined, these molecules make up the majority 
of a cell’s mass. Biological macromolecules are organic, meaning that they 
contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, 
phosphorus, sulfur, and additional minor elements. 


Carbon 


It is often said that life is “carbon-based.” This means that carbon atoms, 
bonded to other carbon atoms or other elements, form the fundamental 
components of many, if not most, of the molecules found uniquely in living 
things. Other elements play important roles in biological molecules, but 
carbon certainly qualifies as the “foundation” element for molecules in 
living things. It is the bonding properties of carbon atoms that are 
responsible for its important role. 


Carbon Bonding 


Carbon contains four electrons in its outer shell. Therefore, it can form four 
covalent bonds with other atoms or molecules. The simplest organic carbon 
molecule is methane (CH), in which four hydrogen atoms bind to a carbon 
atom ([Link]). 


Methane 


Cy 
On” moO 


V4 


Carbon can form four covalent bonds to 
create an organic molecule. The simplest 
carbon molecule is methane (CH,), depicted 
here. 


However, structures that are more complex are made using carbon. Any of 
the hydrogen atoms can be replaced with another carbon atom covalently 
bonded to the first carbon atom. In this way, long and branching chains of 
carbon compounds can be made ((link]a). The carbon atoms may bond with 
atoms of other elements, such as nitrogen, oxygen, and phosphorus 
({link]b). The molecules may also form rings, which themselves can link 
with other rings ([link]c). This diversity of molecular forms accounts for the 
diversity of functions of the biological macromolecules and is based to a 
large degree on the ability of carbon to form multiple bonds with itself and 
other atoms. 


HH 
(a) 
Oo H H 
YS tov 
C-C-N 
74 | \ 
HO H H 
(b) 
i 
H-C-OH 
H ¢ e H 
‘c H Bt 7 
7 N 
HO SY YH H ff OH 
7 \ 
H OH 


(c) 


These examples show three 
molecules (found in living 
organisms) that contain carbon 
atoms bonded in various ways 
to other carbon atoms and the 
atoms of other elements. (a) 
This molecule of stearic acid 
has a long chain of carbon 
atoms. (b) Glycine, a 
component of proteins, contains 
carbon, nitrogen, oxygen, and 
hydrogen atoms. (c) Glucose, a 
sugar, has a ring of carbon 
atoms and one oxygen atom. 


Carbohydrates 


Carbohydrates are macromolecules with which most consumers are 
somewhat familiar. To lose weight, some individuals adhere to “low-carb” 
diets. Athletes, in contrast, often “carb-load” before important competitions 
to ensure that they have sufficient energy to compete at a high level. 
Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and 
vegetables are all natural sources of carbohydrates. Carbohydrates provide 
energy to the body, particularly through glucose, a simple sugar. 
Carbohydrates also have other important functions in humans, animals, and 
plants. 


Carbohydrates can be represented by the formula (CH»O),, where n is the 
number of carbon atoms in the molecule. In other words, the ratio of carbon 
to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates 
are classified into three subtypes: monosaccharides, disaccharides, and 
polysaccharides. 


Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, 
the most common of which is glucose. In monosaccharides, the number of 
carbon atoms usually ranges from three to six. Most monosaccharide names 
end with the suffix -ose. Depending on the number of carbon atoms in the 
sugar, they may be known as trioses (three carbon atoms), pentoses (five 
carbon atoms), and hexoses (six carbon atoms). 


Monosaccharides may exist as a linear chain or as ring-shaped molecules; 
in aqueous solutions, they are usually found in the ring form. 


The chemical formula for glucose is CgH, Og. In most living species, 
glucose is an important source of energy. During cellular respiration, energy 
is released from glucose, and that energy is used to help make adenosine 
triphosphate (ATP). Plants synthesize glucose using carbon dioxide and 
water by the process of photosynthesis, and the glucose, in turn, is used for 
the energy requirements of the plant. The excess synthesized glucose is 
often stored as starch that is broken down by other organisms that feed on 
plants. 


Galactose (part of lactose, or milk sugar) and fructose (found in fruit) are 
other common monosaccharides. Although glucose, galactose, and fructose 
all have the same chemical formula (CgH, Og), they differ structurally and 


chemically (and are known as isomers) because of differing arrangements 
of atoms in the carbon chain ([link)). 


Glucose Galactose Fructose 


Glucose, galactose, and fructose are 
isomeric monosaccharides, meaning that 
they have the same chemical formula but 

slightly different structures. 


Disaccharides (di- = “two”) form when two monosaccharides undergo a 
dehydration reaction (a reaction in which the removal of a water molecule 
occurs). During this process, the hydroxyl group (OH) of one 
monosaccharide combines with a hydrogen atom of another 
monosaccharide, releasing a molecule of water (H»O) and forming a 
covalent bond between atoms in the two sugar molecules. 


Common disaccharides include lactose, maltose, and sucrose. Lactose is a 
disaccharide consisting of the monomers glucose and galactose. It is found 
naturally in milk. Maltose, or malt sugar, is a disaccharide formed from a 
dehydration reaction between two glucose molecules. The most common 


disaccharide is sucrose, or table sugar, which is composed of the monomers 
glucose and fructose. 


A long chain of monosaccharides linked by covalent bonds is known as a 
polysaccharide (poly- = “many”). The chain may be branched or 
unbranched, and it may contain different types of monosaccharides. 
Polysaccharides may be very large molecules. Starch, glycogen, cellulose, 
and chitin are examples of polysaccharides. 


Starch is the stored form of sugars in plants and is made up of amylose and 
amylopectin (both polymers of glucose). Plants are able to synthesize 
glucose, and the excess glucose is stored as starch in different plant parts, 
including roots and seeds. The starch that is consumed by animals is broken 
down into smaller molecules, such as glucose. The cells can then absorb the 
glucose. 


Glycogen is the storage form of glucose in humans and other vertebrates, 
and is made up of monomers of glucose. Glycogen is the animal equivalent 
of starch and is a highly branched molecule usually stored in liver and 
muscle cells. Whenever glucose levels decrease, glycogen is broken down 
to release glucose. 


Cellulose is one of the most abundant natural biopolymers. The cell walls 
of plants are mostly made of cellulose, which provides structural support to 
the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made 
up of glucose monomers that are linked by bonds between particular carbon 
atoms in the glucose molecule. 


Every other glucose monomer in cellulose is flipped over and packed 
tightly as extended long chains. This gives cellulose its rigidity and high 
tensile strength—which is so important to plant cells. Cellulose passing 
through our digestive system is called dietary fiber. While the glucose- 
glucose bonds in cellulose cannot be broken down by human digestive 
enzymes, herbivores such as cows, buffalos, and horses are able to digest 
grass that is rich in cellulose and use it as a food source. In these animals, 
certain species of bacteria reside in the rumen (part of the digestive system 
of herbivores) and secrete the enzyme cellulase. The appendix also contains 
bacteria that break down cellulose, giving it an important role in the 


digestive systems of ruminants. Cellulases can break down cellulose into 
glucose monomers that can be used as an energy source by the animal. 


Carbohydrates serve other functions in different animals. Arthropods, such 
as insects, spiders, and crabs, have an outer skeleton, called the 
exoskeleton, which protects their internal body parts. This exoskeleton is 
made of the biological macromolecule chitin, which is a nitrogenous 
carbohydrate. It is made of repeating units of a modified sugar containing 
nitrogen. 


Thus, through differences in molecular structure, carbohydrates are able to 
serve the very different functions of energy storage (starch and glycogen) 
and structural support and protection (cellulose and chitin) ([link]). 


Starch Glycogen 
jes ao cc. jie CH2OH 
OH *O 
Ss 
OH ’ 
Cellulose Chitin 
CH20OH OH CH20H OH 


O. CH OCH 
te) fe) ‘ La ‘ a 
HO ie) Oo Oo yin ‘de 
OH CH2OH OH CH, bins 
3 fe) ag OH 


CH20H CH2OH 


Bs e 
O Ch; O Ch; 


Although their structures and functions differ, all 
polysaccharide carbohydrates are made up of 
monosaccharides and have the chemical formula 
(CH»O)n. 


Lipids 


Lipids include a diverse group of compounds that are united by a common 
feature. Lipids are hydrophobic (“water-fearing”), or insoluble in water, 
because they are nonpolar molecules. This is because they are hydrocarbons 
that include only nonpolar carbon-carbon or carbon-hydrogen bonds. Lipids 
perform many different functions in a cell. Cells store energy for long-term 
use in the form of lipids called fats. Lipids also provide insulation from the 
environment for plants and animals ({link]). For example, they help keep 
aquatic birds and mammals dry because of their water-repelling nature. 
Lipids are also the building blocks of many hormones and are an important 
constituent of the plasma membrane. Lipids include fats, oils, waxes, 
phospholipids, and steroids. 


Hydrophobic lipids in the fur of 
aquatic mammals, such as this river 
otter, protect them from the elements. 
(credit: Ken Bosma) 


A fat molecule, such as a triglyceride, consists of two main components— 
glycerol and fatty acids. Glycerol is an organic compound with three carbon 
atoms, five hydrogen atoms, and three hydroxyl (-OH) groups. Fatty acids 
have a long chain of hydrocarbons to which an acidic carboxyl group is 
attached, hence the name “fatty acid.” The number of carbons in the fatty 
acid is normally 12-18 carbons. In a fat molecule, a fatty acid is attached to 
each of the three oxygen atoms in the -OH groups of the glycerol molecule 
with a covalent bond ({link]). 


Saturated fatty acid Triglyceride 
H H H H H ‘3 ig c ag 
Cc Cc Cc Cc CH 
HO RR Rt MeN ON NN 
CG CG GC G G H—-C—O* H2 H2 Hp Hp 
| 2 2 He 2 2 Hp Hp Hp H 
fe) le ti 
ae 
H-—C-—O Ho H2 Hp H2 
Ct Oe Oe cK 
r i , ee ee ae ae ee 
insaturated fatty aci HAC ae H—-¢—07 Ho Hp Hp Hp 
H 
CH, 
HC 
i fe 
Spe ee Ne a ee bee Seti 
i Ha Hi Hy Fi 7 
ie) te He CH3 Hp 
H2C Cc 
‘ ne a \ 
CH2 H CH2 
O- Phospholipid 7 es c cc. / 
I H2C A NAAAN, “A Oe 
O-—P—O-CH, | Hee” “ec HC 
8 a | I! lL 
He ee ae ee 
{e) Ho He Ho Ho | § 
Nc C C Cc Cc CH H Me 
Sy eS 
H2 Hp Hz He He 
CN H> Ho Hp Hp Ho Hp Hp He 
eRe a ee ee ee 
ao— Cc Cc Cc Cc c Cc Cc Cc CH; 
Ho Ho Ho Ho He H2 Ha He 


Lipids include fats, such as triglycerides, which are made 
up of fatty acids and glycerol, phospholipids, and 
steroids. 


During this covalent bond formation, three water molecules are released. 
The three fatty acids in the fat may be similar or dissimilar. These fats are 


also called triglycerides because they have three fatty acids. Some fatty 
acids have common names that specify their origin. For example, palmitic 
acid, a saturated fatty acid, is derived from the palm tree. Arachidic acid is 
derived from Arachis hypogaea, the scientific name for peanuts. 


Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there 
are only single bonds between neighboring carbons in the hydrocarbon 
chain, the fatty acid is saturated. Saturated fatty acids are saturated with 
hydrogen; in other words, the number of hydrogen atoms attached to the 
carbon skeleton is maximized. 


When the hydrocarbon chain contains a double bond, the fatty acid is an 
unsaturated fatty acid. 


Most unsaturated fats are liquid at room temperature and are called oils. If 
there is one double bond in the molecule, then it is known as a 
monounsaturated fat (e.g., olive oil), and if there is more than one double 
bond, then it is known as a polyunsaturated fat (e.g., canola oil). 


Saturated fats tend to get packed tightly and are solid at room temperature. 
Animal fats with stearic acid and palmitic acid contained in meat, and the 
fat with butyric acid contained in butter, are examples of saturated fats. 
Mammals store fats in specialized cells called adipocytes, where globules of 
fat occupy most of the cell. In plants, fat or oil is stored in seeds and is used 
as a source of energy during embryonic development. 


Unsaturated fats or oils are usually of plant origin and contain unsaturated 
fatty acids. The double bond causes a bend or a “kink” that prevents the 
fatty acids from packing tightly, keeping them liquid at room temperature. 
Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated 
fats. Unsaturated fats help to improve blood cholesterol levels, whereas 
saturated fats contribute to plaque formation in the arteries, which increases 
the risk of a heart attack. 


In the food industry, oils are artificially hydrogenated to make them semi- 
solid, leading to less spoilage and increased shelf life. Simply speaking, 
hydrogen gas is bubbled through oils to solidify them. During this 
hydrogenation process, double bonds of the cis-conformation in the 


hydrocarbon chain may be converted to double bonds in the trans- 
conformation. This forms a trans-fat from a cis-fat. The orientation of the 
double bonds affects the chemical properties of the fat ((link]). 


trans-fat molecule 


During the hydrogenation process, 
the orientation around the double 
bonds is changed, making a trans- 
fat from a cis-fat. This changes the 
chemical properties of the 
molecule. 


Margarine, some types of peanut butter, and shortening are examples of 
artificially hydrogenated trans-fats. Recent studies have shown that an 
increase in trans-fats in the human diet may lead to an increase in levels of 
low-density lipoprotein (LDL), or “bad” cholesterol, which, in turn, may 
lead to plaque deposition in the arteries, resulting in heart disease. Many 
fast food restaurants have recently eliminated the use of trans-fats, and U.S. 
food labels are now required to list their trans-fat content. 


Essential fatty acids are fatty acids that are required but not synthesized by 
the human body. Consequently, they must be supplemented through the 


diet. Omega-3 fatty acids fall into this category and are one of only two 
known essential fatty acids for humans (the other being omega-6 fatty 
acids). They are a type of polyunsaturated fat and are called omega-3 fatty 
acids because the third carbon from the end of the fatty acid participates in 
a double bond. 


Salmon, trout, and tuna are good sources of omega-3 fatty acids. Omega-3 
fatty acids are important in brain function and normal growth and 
development. They may also prevent heart disease and reduce the risk of 
cancer. 


Like carbohydrates, fats have received a lot of bad publicity. It is true that 
eating an excess of fried foods and other “fatty” foods leads to weight gain. 
However, fats do have important functions. Fats serve as long-term energy 
storage. They also provide insulation for the body. Therefore, “healthy” 
unsaturated fats in moderate amounts should be consumed on a regular 
basis. 


Phospholipids are the major constituent of the plasma membrane. Like 
fats, they are composed of fatty acid chains attached to a glycerol or similar 
backbone. Instead of three fatty acids attached, however, there are two fatty 
acids and the third carbon of the glycerol backbone is bound to a phosphate 
group. The phosphate group is modified by the addition of an alcohol. 


A phospholipid has both hydrophobic and hydrophilic regions. The fatty 
acid chains are hydrophobic and exclude themselves from water, whereas 
the phosphate is hydrophilic and interacts with water. 


Cells are surrounded by a membrane, which has a bilayer of phospholipids. 
The fatty acids of phospholipids face inside, away from water, whereas the 

phosphate group can face either the outside environment or the inside of the 
cell, which are both aqueous. 


Steroids and Waxes 


Unlike the phospholipids and fats discussed earlier, steroids have a ring 
structure. Although they do not resemble other lipids, they are grouped with 
them because they are also hydrophobic. All steroids have four, linked 
carbon rings and several of them, like cholesterol, have a short tail. 


Cholesterol is a steroid. Cholesterol is mainly synthesized in the liver and is 
the precursor of many steroid hormones, such as testosterone and estradiol. 
It is also the precursor of vitamins E and K. Cholesterol is the precursor of 
bile salts, which help in the breakdown of fats and their subsequent 
absorption by cells. Although cholesterol is often spoken of in negative 
terms, it is necessary for the proper functioning of the body. It is a key 
component of the plasma membranes of animal cells. 


Waxes are made up of a hydrocarbon chain with an alcohol (-OH) group 
and a fatty acid. Examples of animal waxes include beeswax and lanolin. 
Plants also have waxes, such as the coating on their leaves, that helps 
prevent them from drying out. 


Note: 

Concept in Action 
fl [m 
' = 


i. 


fas 
mess’ OPENStAX COLLEGE” 
— 
_— 

*e . 
i eae 


For an additional perspective on lipids, explore “Biomolecules: The 
Lipids” through this interactive animation. 


Proteins 


Proteins are one of the most abundant organic molecules in living systems 
and have the most diverse range of functions of all macromolecules. 


Proteins may be structural, regulatory, contractile, or protective; they may 
serve in transport, storage, or membranes; or they may be toxins or 
enzymes. Each cell in a living system may contain thousands of different 
proteins, each with a unique function. Their structures, like their functions, 
vary greatly. They are all, however, polymers of amino acids, arranged in a 
linear sequence. 


The functions of proteins are very diverse because there are 20 different 
chemically distinct amino acids that form long chains, and the amino acids 
can be in any order. For example, proteins can function as enzymes or 
hormones. Enzymes, which are produced by living cells, are catalysts in 
biochemical reactions (like digestion) and are usually proteins. Each 
enzyme is specific for the substrate (a reactant that binds to an enzyme) 
upon which it acts. Enzymes can function to break molecular bonds, to 
rearrange bonds, or to form new bonds. An example of an enzyme is 
salivary amylase, which breaks down amylose, a component of starch. 


Hormones are chemical signaling molecules, usually proteins or steroids, 
secreted by an endocrine gland or group of endocrine cells that act to 
control or regulate specific physiological processes, including growth, 
development, metabolism, and reproduction. For example, insulin is a 
protein hormone that maintains blood glucose levels. 


Proteins have different shapes and molecular weights; some proteins are 
globular in shape whereas others are fibrous in nature. For example, 
hemoglobin is a globular protein, but collagen, found in our skin, is a 
fibrous protein. Protein shape is critical to its function. Changes in 
temperature, pH, and exposure to chemicals may lead to permanent changes 
in the shape of the protein, leading to a loss of function or denaturation (to 
be discussed in more detail later). All proteins are made up of different 
arrangements of the same 20 kinds of amino acids. 


Amino acids are the monomers that make up proteins. Each amino acid has 
the same fundamental structure, which consists of a central carbon atom 
bonded to an amino group (—NHb)), a carboxyl group (-COOH), and a 
hydrogen atom. Every amino acid also has another variable atom or group 
of atoms bonded to the central carbon atom known as the R group. The R 


group is the only difference in structure between the 20 amino acids; 
otherwise, the amino acids are identical ({link]). 


Fundamental structure 


Hydrogen 


group group 
H2N——C——COOH 


H 
Amino | Carboxyl 


Alanine Valine 


H 


H2N—— C—-COOH H2N—— C——COOH 


CHs 


Lysine Aspartic acid 


H 
H2N——C—COOH HaN——C—COOH 
(CHa)4 CH2 


NH2 


Amino acids are made up of a 
central carbon bonded to an 
amino group (—NH>), a 
carboxyl group (-COOH), and a 
hydrogen atom. The central 
carbon’s fourth bond varies 
among the different amino 
acids, as seen in these examples 
of alanine, valine, lysine, and 
aspartic acid. 


The chemical nature of the R group determines the chemical nature of the 
amino acid within its protein (that is, whether it is acidic, basic, polar, or 
nonpolar). 


The sequence and number of amino acids ultimately determine a protein’s 
shape, size, and function. Each amino acid is attached to another amino acid 
by a covalent bond, known as a peptide bond, which is formed by a 
dehydration reaction. The carboxyl group of one amino acid and the amino 
group of a second amino acid combine, releasing a water molecule. The 
resulting bond is the peptide bond. 


The products formed by such a linkage are called polypeptides. While the 
terms polypeptide and protein are sometimes used interchangeably, a 
polypeptide is technically a polymer of amino acids, whereas the term 
protein is used for a polypeptide or polypeptides that have combined 
together, have a distinct shape, and have a unique function. 


Note: 

Evolution in Action 

The Evolutionary Significance of Cytochrome c 

Cytochrome c is an important component of the molecular machinery that 
harvests energy from glucose. Because this protein’s role in producing 
cellular energy is crucial, it has changed very little over millions of years. 
Protein sequencing has shown that there is a considerable amount of 
sequence similarity among cytochrome c molecules of different species; 
evolutionary relationships can be assessed by measuring the similarities or 
differences among various species’ protein sequences. 

For example, scientists have determined that human cytochrome c contains 
104 amino acids. For each cytochrome c molecule that has been sequenced 
to date from different organisms, 37 of these amino acids appear in the 
Same position in each cytochrome c. This indicates that all of these 
organisms are descended from a common ancestor. On comparing the 
human and chimpanzee protein sequences, no sequence difference was 


found. When human and rhesus monkey sequences were compared, a 
single difference was found in one amino acid. In contrast, human-to-yeast 
comparisons show a difference in 44 amino acids, suggesting that humans 
and chimpanzees have a more recent common ancestor than humans and 
the rhesus monkey, or humans and yeast. 


Protein Structure 


As discussed earlier, the shape of a protein is critical to its function. There 
are four levels of protein structure: primary, secondary, tertiary, and 
quatemary ({link]). 


The unique sequence and number of amino acids in a polypeptide chain is 
its primary structure. The unique sequence for every protein is ultimately 
determined by the gene that encodes the protein. Any change in the gene 
sequence may lead to a different amino acid being added to the polypeptide 
chain, causing a change in protein structure and function. 


In nature, some proteins are formed from several polypeptides, also known 
as subunits, and the interaction of these subunits forms the quaternary 
structure. Weak interactions between the subunits help to stabilize the 
overall structure. For example, hemoglobin is a combination of four 
polypeptide subunits. 


Amino acids 
Primary protein structure 
sequence of a chain of 
amino acids 
Beta-pleated Alpha helix Secondary protein structure 
sheet hydrogen bonding of the peptide 
backbone causes the amino 
> acids to fold into a repeating 
| pattern 


Beta-pleated Tertiary protein structure 

sheet three-dimensional folding 
pattern of a protein due to side 
chain interactions 

Alpha helix 


Qo 


Lo 


The four levels of protein structure can 
be observed in these illustrations. (credit: 
modification of work by National Human 

Genome Research Institute) 


Quaternary protein structure 
protein consisting of more 
than one amino acid chain 


Each protein has its own unique sequence and shape held together by 
chemical interactions. If the protein is subject to changes in temperature, 
pH, or exposure to chemicals, the protein structure may change, losing its 
shape in what is known as denaturation as discussed earlier. Denaturation is 
often reversible because the primary structure is preserved if the denaturing 
agent is removed, allowing the protein to resume its function. Sometimes 
denaturation is irreversible, leading to a loss of function. One example of 


protein denaturation can be seen when an egg is fried or boiled. The 
albumin protein in the liquid egg white is denatured when placed in a hot 
pan, changing from a clear substance to an opaque white substance. Not all 
proteins are denatured at high temperatures; for instance, bacteria that 
survive in hot springs have proteins that are adapted to function at those 
temperatures. 


Note: 
Concept in Action 


Detain es a 


— : 
meee, <OPENStAX COLLEGE 


For an additional perspective on proteins, explore “Biomolecules: The 
Proteins” through this interactive animation. 


Nucleic Acids 


Nucleic acids are key macromolecules in the continuity of life. They carry 
the genetic blueprint of a cell and carry instructions for the functioning of 
the cell. 


The two main types of nucleic acids are deoxyribonucleic acid (DNA) and 
ribonucleic acid (RNA). DNA is the genetic material found in all living 
organisms, ranging from single-celled bacteria to multicellular mammals. 


The other type of nucleic acid, RNA, is mostly involved in protein 
synthesis. The DNA molecules never leave the nucleus, but instead use an 
RNA intermediary to communicate with the rest of the cell. Other types of 
RNA are also involved in protein synthesis and its regulation. 


DNA and RNA are made up of monomers known as nucleotides. The 
nucleotides combine with each other to form a polynucleotide, DNA or 
RNA. Each nucleotide is made up of three components: a nitrogenous base, 
a pentose (five-carbon) sugar, and a phosphate group ([link]). Each 
nitrogenous base in a nucleotide is attached to a sugar molecule, which is 
attached to a phosphate group. 


NH> 


N 
Nitrogenous base 


Il 

OF 7 O-——— GH fe) 
Oo 

Phosphate 


OH 
Sugar 


A nucleotide is made up of three 
components: a nitrogenous base, a 
pentose sugar, and a phosphate group. 


DNA Double-Helical Structure 


DNA has a double-helical structure ({link]). It is composed of two strands, 
or polymers, of nucleotides. The strands are formed with bonds between 
phosphate and sugar groups of adjacent nucleotides. The strands are bonded 
to each other at their bases with hydrogen bonds, and the strands coil about 
each other along their length, hence the “double helix” description, which 
means a double spiral. 


The double-helix 
model shows DNA 
as two parallel 
strands of 


intertwining 
molecules. (credit: 
Jerome Walker, 
Dennis Myts) 


The alternating sugar and phosphate groups lie on the outside of each 
strand, forming the backbone of the DNA. The nitrogenous bases are 
stacked in the interior, like the steps of a staircase, and these bases pair; the 
pairs are bound to each other by hydrogen bonds. The bases pair in such a 
way that the distance between the backbones of the two strands is the same 
all along the molecule. 


Section Summary 


Living things are carbon-based because carbon plays such a prominent role 
in the chemistry of living things. The four covalent bonding positions of the 
carbon atom can give rise to a wide diversity of compounds with many 
functions, accounting for the importance of carbon in living things. 
Carbohydrates are a group of macromolecules that are a vital energy source 
for the cell, provide structural support to many organisms, and can be found 


on the surface of the cell as receptors or for cell recognition. Carbohydrates 
are classified as monosaccharides, disaccharides, and polysaccharides, 
depending on the number of monomers in the molecule. 


Lipids are a class of macromolecules that are nonpolar and hydrophobic in 
nature. Major types include fats and oils, waxes, phospholipids, and 
steroids. Fats and oils are a stored form of energy and can include 
triglycerides. Fats and oils are usually made up of fatty acids and glycerol. 


Proteins are a class of macromolecules that can perform a diverse range of 
functions for the cell. They help in metabolism by providing structural 
support and by acting as enzymes, carriers or as hormones. The building 
blocks of proteins are amino acids. Proteins are organized at four levels: 
primary, secondary, tertiary, and quaternary. Protein shape and function are 
intricately linked; any change in shape caused by changes in temperature, 
pH, or chemical exposure may lead to protein denaturation and a loss of 
function. 


Nucleic acids are molecules made up of repeating units of nucleotides that 
direct cellular activities such as cell division and protein synthesis. Each 
nucleotide is made up of a pentose sugar, a nitrogenous base, and a 
phosphate group. There are two types of nucleic acids: DNA and RNA. 


Glossary 


amino acid 
a monomer of a protein 


carbohydrate 
a biological macromolecule in which the ratio of carbon to hydrogen to 
oxygen is 1:2:1; carbohydrates serve as energy sources and structural 
support in cells 


cellulose 
a polysaccharide that makes up the cell walls of plants and provides 
structural support to the cell 


chitin 


a type of carbohydrate that forms the outer skeleton of arthropods, 
such as insects and crustaceans, and the cell walls of fungi 


denaturation 
the loss of shape in a protein as a result of changes in temperature, pH, 
or exposure to chemicals 


deoxyribonucleic acid (DNA) 
a double-stranded polymer of nucleotides that carries the hereditary 
information of the cell 


disaccharide 
two sugar monomers that are linked together by a peptide bond 


enzyme 
a catalyst in a biochemical reaction that is usually a complex or 
conjugated protein 


fat 
a lipid molecule composed of three fatty acids and a glycerol 
(triglyceride) that typically exists in a solid form at room temperature 


glycogen 
a storage carbohydrate in animals 


hormone 
a chemical signaling molecule, usually a protein or steroid, secreted by 
an endocrine gland or group of endocrine cells; acts to control or 
regulate specific physiological processes 


lipids 
a class of macromolecules that are nonpolar and insoluble in water 
macromolecule 


a large molecule, often formed by polymerization of smaller 
monomers 


monosaccharide 


a single unit or monomer of carbohydrates 


nucleic acid 
a biological macromolecule that carries the genetic information of a 
cell and carries instructions for the functioning of the cell 


nucleotide 
a monomer of nucleic acids; contains a pentose sugar, a phosphate 
group, and a nitrogenous base 


oil 
an unsaturated fat that is a liquid at room temperature 


phospholipid 
a major constituent of the membranes of cells; composed of two fatty 
acids and a phosphate group attached to the glycerol backbone 


polypeptide 
a long chain of amino acids linked by peptide bonds 


polysaccharide 
a long chain of monosaccharides; may be branched or unbranched 


protein 
a biological macromolecule composed of one or more chains of amino 
acids 


ribonucleic acid (RNA) 
a single-stranded polymer of nucleotides that is involved in protein 
synthesis 


saturated fatty acid 
a long-chain hydrocarbon with single covalent bonds in the carbon 
chain; the number of hydrogen atoms attached to the carbon skeleton is 
maximized 


starch 
a storage carbohydrate in plants 


steroid 
a type of lipid composed of four fused hydrocarbon rings 


trans-fat 
a form of unsaturated fat with the hydrogen atoms neighboring the 
double bond across from each other rather than on the same side of the 
double bond 


triglyceride 
a fat molecule; consists of three fatty acids linked to a glycerol 
molecule 


unsaturated fatty acid 
a long-chain hydrocarbon that has one or more than one double bonds 
in the hydrocarbon chain 


Introduction Cells EnBio 
class="introduction" 


(a) Nasal 
sinus cells 
(viewed with 
a light 
microscope), 
(b) onion 
cells (viewed 
with a light 
microscope), 
and (c) Vibrio 
tasmaniensis 
bacterial cells 
(viewed using 
a scanning 
electron 
microscope) 
are from very 
different 
organisms, 
yet all share 
certain 
characteristic 
s of basic cell 
structure. 
(credit a: 
modification 
of work by 
Ed Uthman, 
MD; credit b: 
modification 
of work by 
Umberto 
Salvagnin; 
credit c: 


modification 
of work by 
Anthony 
D'Onofrio; 
scale-bar data 
from Matt 
Russell) 


Close your eyes and picture a brick wall. What is the basic building block 
of that wall? It is a single brick, of course. Like a brick wall, your body is 
composed of basic building blocks, and the building blocks of your body 

are cells. 


Your body has many kinds of cells, each specialized for a specific purpose. 
Just as a home is made from a variety of building materials, the human 
body is constructed from many cell types. For example, epithelial cells 
protect the surface of the body and cover the organs and body cavities 
within. Bone cells help to support and protect the body. Cells of the immune 
system fight invading bacteria. Additionally, red blood cells carry oxygen 
throughout the body. Each of these cell types plays a vital role during the 
growth, development, and day-to-day maintenance of the body. In spite of 
their enormous variety, however, all cells share certain fundamental 
characteristics. 


How Cells Are Studied EnBio 
By the end of this section, you will be able to: 


¢ Describe the roles of cells in organisms 
e Summarize the cell theory 


A cell is the smallest unit of a living thing. A living thing, like you, is called 
an organism. Thus, cells are the basic building blocks of all organisms. 


In multicellular organisms, several cells of one particular kind interconnect 
with each other and perform shared functions to form tissues (for example, 
muscle tissue, connective tissue, and nervous tissue), several tissues 
combine to form an organ (for example, stomach, heart, or brain), and 
several organs make up an organ system (such as the digestive system, 
circulatory system, or nervous system). Several systems functioning 
together form an organism (such as an elephant, for example). 


There are many types of cells, and all are grouped into one of two broad 
categories: prokaryotic and eukaryotic. Animal cells, plant cells, fungal 
cells, and protist cells are classified as eukaryotic, whereas bacteria and 
archaea cells are classified as prokaryotic. Before discussing the criteria for 
determining whether a cell is prokaryotic or eukaryotic, let us first examine 
how biologists study cells. 


Microscopy 


Cells vary in size. With few exceptions, individual cells are too small to be 
seen with the naked eye, so scientists use microscopes to study them. A 
microscope is an instrument that magnifies an object. Most images of cells 
are taken with a microscope and are called micrographs. 


Light Microscopes 


Light microscopes commonly used in the undergraduate college laboratory 
magnify up to approximately 400 times. Two parameters that are important 
in microscopy are magnification and resolving power. Magnification is the 


degree of enlargement of an object. Resolving power is the ability of a 
microscope to allow the eye to distinguish two adjacent structures as 
separate; the higher the resolution, the closer those two objects can be, and 
the better the clarity and detail of the image. When oil immersion lenses are 
used, magnification is usually increased to 1,000 times for the study of 
smaller cells, like most prokaryotic cells. 


Note: 
Concept in Action 


arc 


= ocr, 
meee <OPENStAX COLLEGE” 


For another perspective on cell size, try the HowBig interactive. 


A second type of microscope used in laboratories is the dissecting 
microscope ({link]b). These microscopes have a lower magnification (20 to 
80 times the object size) than light microscopes and can provide a three- 
dimensional view of the specimen. Thick objects can be examined with 
many components in focus at the same time. 


Eyepieces 
Eyepieces 


Objectives 
(magnification 
control) 


Focus 


j Top light 
Objective 


Stage 


Stage 


Coarse 
focus 


Fine 
focus 
Light 
source 


Bottom 
light 
source 


(b) 


(a) Most light microscopes used in a college biology lab can 
magnify cells up to approximately 400 times. (b) Dissecting 
microscopes have a lower magnification than light microscopes 
and are used to examine larger objects, such as tissues. 


Cell Theory 


By the late 1830s, botanist Matthias Schleiden and zoologist Theodor 
Schwann were studying tissues and proposed the unified cell theory, which 
states that all living things are composed of one or more cells, that the cell 
is the basic unit of life, and that all new cells arise from existing cells. 
These principles still stand today. 


Section Summary 


A cell is the smallest unit of life. Most cells are so small that they cannot be 
viewed with the naked eye. Therefore, scientists must use microscopes to 
study cells. Electron microscopes provide higher magnification, higher 
resolution, and more detail than light microscopes. The unified cell theory 


states that all organisms are composed of one or more cells, the cell is the 
basic unit of life, and new cells arise from existing cells. 


Glossary 


microscope 
the instrument that magnifies an object 


unified cell theory 
the biological concept that states that all organisms are composed of 
one or more cells, the cell is the basic unit of life, and new cells arise 
from existing cells 


Comparing Prokaryotic and Eukaryotic Cells EnBio 
By the end of this section, you will be able to: 


e Name examples of prokaryotic and eukaryotic organisms 
e Compare and contrast prokaryotic cells and eukaryotic cells 
¢ Describe the relative sizes of different kinds of cells 


Cells fall into one of two broad categories: prokaryotic and eukaryotic. The 
predominantly single-celled organisms of the domains Bacteria and 
Archaea are classified as prokaryotes (pro- = before; -karyon- = nucleus). 
Animal cells, plant cells, fungi, and protists are eukaryotes (eu- = true). 


Components of Prokaryotic Cells 


All cells share four common components: 1) a plasma membrane, an outer 
covering that separates the cell’s interior from its surrounding environment; 
2) cytoplasm, consisting of a jelly-like region within the cell in which other 
cellular components are found; 3) DNA, the genetic material of the cell; and 
4) ribosomes, particles that synthesize proteins. However, prokaryotes differ 
from eukaryotic cells in several ways. 


A prokaryotic cell is a simple, single-celled (unicellular) organism that 
lacks a nucleus, or any other membrane-bound organelle. We will shortly 
come to see that this is significantly different in eukaryotes. Prokaryotic 
DNA is found in the central part of the cell: a darkened region called the 
nucleoid ([link]). 


Cell 
membrane 


Chromosome Nucleoid region 
(DNA) 


This figure shows the generalized 
structure of a prokaryotic cell. 


Eukaryotic Cells 


A eukaryotic cell is a cell that has a membrane-bound nucleus and other 
membrane-bound compartments or sacs, called organelles, which have 
specialized functions. The word eukaryotic means “true kernel” or “true 
nucleus,” alluding to the presence of the membrane-bound nucleus in these 
cells. The word “organelle” means “little organ,” and, as already mentioned, 
organelles have specialized cellular functions, just as the organs of your 
body have specialized functions. 


Cell Size 


At 0.1-5.0 pm in diameter, prokaryotic cells are significantly smaller than 
eukaryotic cells, which have diameters ranging from 10—100 pm ({link)). 
The small size of prokaryotes allows ions and organic molecules that enter 
them to quickly spread to other parts of the cell. Similarly, any wastes 
produced within a prokaryotic cell can quickly move out. However, larger 
eukaryotic cells have evolved different structural adaptations to enhance 
cellular transport. Indeed, the large size of these cells would not be possible 


without these adaptations. In general, cell size is limited because volume 
increases much more quickly than does cell surface area. As a cell becomes 
larger, it becomes more and more difficult for the cell to acquire sufficient 
materials to support the processes inside the cell, because the relative size 
of the surface area across which materials must be transported declines. 


Animal 
cell 


Mitochondria 


Protein 


Ostrich Adult 
Bacteria egg female 


0.1 nm inm 10 nm 100 nm 1yum 10 um 100 pm 1mm 10 mm 100 mm 1m 


Naked eye 


a 


Light microscope 


Electron microscope 


This figure shows the relative sizes of different kinds of cells 
and cellular components. An adult human is shown for 
comparison. 


Section Summary 


Prokaryotes are predominantly single-celled organisms of the domains 
Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, 
ribosomes, a cell wall, DNA, and lack membrane-bound organelles. Many 
also have polysaccharide capsules. Prokaryotic cells range in diameter from 
0.1—5.0 pm. 


Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, 
cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a 
prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a 
membrane), and has other membrane-bound organelles that allow for 
compartmentalization of functions. Eukaryotic cells tend to be 10 to 100 
times the size of prokaryotic cells. 


Glossary 


eukaryotic cell 
a cell that has a membrane-bound nucleus and several other 
membrane-bound compartments or sacs 


organelle 
a membrane-bound compartment or sac within a cell 


prokaryotic cell 
a unicellular organism that lacks a nucleus or any other membrane- 
bound organelle 


Eukaryotic Cells EnBio 
By the end of this section, you will be able to: 


e Describe the structure of eukaryotic plant and animal cells 
e State the role of the plasma membrane 


At this point, it should be clear that eukaryotic cells have a more complex 
structure than do prokaryotic cells. Organelles allow for various functions 
to occur in the cell at the same time. Before discussing the functions of 
organelles within a eukaryotic cell, let us first examine two important 
components of the cell: the plasma membrane and the cytoplasm. 


Note: 
Art Connection 


This figure shows (a) a typical animal cell and (b) a typical plant cell. 


Nucleus Cytoskeleton 
Nuclear envelope: Microtubules: form the 
membrane enclosing mitotic spindle and 
the nucleus. Protein-lined maintain cell shape. 
pores allow material to Centrosome: microtubule- 
move in and out. organizing center. 
Chromatin: DNA plus Intermediate filaments: 
associated proteins. fibrous proteins that hold 
Nucleolus: organelles in place. 


condensed region Microfilaments: 
where ribosomes fibrous proteins; 


are formed. form the cellular 
Peroxisome: Plasma 
metabolizes membrane 
waste 
Lysosome: 


digests food and 
waste materials. 


Golgi apparatus: 


5 modifies proteins. 
Endoplasmic 


reticulum 
Rough: associated 
with ribosomes; 
makes secretory and 
membrane proteins. 
Smooth: makes lipids. 


Cytoplasm 


Mitochondria: 
produce energy. 


Plasmodesmata: Endoplasmic reticulum Nucleus: contains 
channels connect smooth rough chromatin, a 

two plant cells nuclear envelope, 
and a nucleolus, 
as in an animal cell 


Cell wall: maintains 
cell shape 


Plasma 
membrane 


Cytoplasm 


Central vacuole: 
filled with cell sap 
that maintains 
pressure against 
cell wall 
Mitochondria 


Cytoskeleton: 
microtubules Peroxisome 
intermediate 

filaments Chloroplast: site Plastid: stores 
microfilaments of photosynthesis pigments 


(b) 


The Plasma Membrane 


Like prokaryotes, eukaryotic cells have a plasma membrane ((link]) made 
up of a phospholipid bilayer with embedded proteins that separates the 
internal contents of the cell from its surrounding environment. A 
phospholipid is a lipid molecule composed of two fatty acid chains, a 
glycerol backbone, and a phosphate group. The plasma membrane regulates 
the passage of some substances, such as organic molecules, ions, and water, 
preventing the passage of some to maintain internal conditions, while 
actively bringing in or removing others. Other compounds move passively 


across the membrane. 


Glycoprotein: protein with Glycolipid: lipid with 
Fas ; Pa carbohydrate 
attached 


carbohydrate attached 


Peripheral membrane Phospholipid 
ilay 


protein Pi ple 
Integral membrane Cholesterol P 
protein \ Protein channel 


Filaments of the cytoskeleton 


The plasma membrane is a phospholipid bilayer 
with embedded proteins. There are other 
components, such as cholesterol and 
carbohydrates, which can be found in the 
membrane in addition to phospholipids and 
protein. 


The Cytoplasm 


The cytoplasm comprises the contents of a cell between the plasma 
membrane and the nuclear envelope (a structure to be discussed shortly). It 
is made up of organelles suspended in the gel-like cytosol, the cytoskeleton, 
and various chemicals ([link]). Even though the cytoplasm consists of 70 to 
80 percent water, it has a semi-solid consistency, which comes from the 
proteins within it. However, proteins are not the only organic molecules 
found in the cytoplasm. Glucose and other simple sugars, polysaccharides, 
amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found 
there too. Ions of sodium, potassium, calcium, and many other elements are 
also dissolved in the cytoplasm. Many metabolic reactions, including 
protein synthesis, take place in the cytoplasm. 


The Cytoskeleton 


If you were to remove all the organelles from a cell, would the plasma 
membrane and the cytoplasm be the only components left? No. Within the 
cytoplasm, there would still be ions and organic molecules, plus a network 
of protein fibers that helps to maintain the shape of the cell, secures certain 
organelles in specific positions, allows cytoplasm and vesicles to move 
within the cell, and enables unicellular organisms to move independently. 
Collectively, this network of protein fibers is known as the cytoskeleton. 


Flagella and Cilia 


Flagella (singular = flagellum) are long, hair-like structures that extend 
from the plasma membrane and are used to move an entire cell, (for 
example, sperm, Euglena). When present, the cell has just one flagellum or 
a few flagella. When cilia (singular = cilium) are present, however, they are 
many in number and extend along the entire surface of the plasma 
membrane. They are short, hair-like structures that are used to move entire 
cells (such as paramecium) or move substances along the outer surface of 
the cell (for example, the cilia of cells lining the fallopian tubes that move 
the ovum toward the uterus, or cilia lining the cells of the respiratory tract 
that move particulate matter toward the throat that mucus has trapped). 


The Endomembrane System 


The Nucleus 


Typically, the nucleus is the most prominent organelle in a cell ((link]). The 
nucleus (plural = nuclei) houses the cell’s DNA in the form of chromatin 
and directs the synthesis of ribosomes and proteins. Let us look at it in more 
detail ({Llink]). 


Endoplasmic 
reticulum 


Nucleolus 


Chromatin 


Nucleoplasm 


Nuclear pore 


Nuclear envelope 


The outermost boundary of the 
nucleus is the nuclear envelope. 
Notice that the nuclear envelope 
consists of two phospholipid bilayers 
(membranes)—an outer membrane 
and an inner membrane—in contrast 
to the plasma membrane ((link]), 
which consists of only one 
phospholipid bilayer. (credit: 
modification of work by NIGMS, 
NIH) 


The nuclear envelope is a double-membrane structure that constitutes the 
outermost portion of the nucleus ([link]). Both the inner and outer 
membranes of the nuclear envelope are phospholipid bilayers. 


The nuclear envelope is punctuated with pores that control the passage of 
ions, molecules, and RNA between the nucleoplasm and the cytoplasm. 


To understand chromatin, it is helpful to first consider chromosomes. 
Chromosomes are structures within the nucleus that are made up of DNA, 
the hereditary material, and proteins. This combination of DNA and 
proteins is called chromatin. In eukaryotes, chromosomes are linear 
structures. Every species has a specific number of chromosomes in the 


nucleus of its body cells. For example, in humans, the chromosome number 
is 46, whereas in fruit flies, the chromosome number is eight. 


Mitochondria 


Mitochondria (singular = mitochondrion) are often called the 
“powerhouses” or “energy factories” of a cell because they are responsible 
for making adenosine triphosphate (ATP), the cell’s main energy-carrying 
molecule. The formation of ATP from the breakdown of glucose is known 
as cellular respiration. Mitochondria are oval-shaped, double-membrane 
organelles ({link]) that have their own ribosomes and DNA. Each 
membrane is a phospholipid bilayer embedded with proteins. 


Mitochondrial 
matrix 


Cristae 


Outer 
membrane 


Inner 
membrane 


This transmission electron micrograph shows a 
mitochondrion as viewed with an electron 
microscope. Notice the inner and outer 
membranes, the cristae, and the mitochondrial 
matrix. (credit: modification of work by Matthew 
Britton; scale-bar data from Matt Russell) 


Animal Cells versus Plant Cells 


Despite their fundamental similarities, there are some striking differences 
between animal and plant cells (see [link]). Animal cells have centrioles, 
centrosomes (discussed under the cytoskeleton), and lysosomes, whereas 
plant cells do not. Plant cells have a cell wall, chloroplasts, plasmodesmata, 
and plastids used for storage, and a large central vacuole, whereas animal 
cells do not. 


The Cell Wall 


In [link]b, the diagram of a plant cell, you see a structure external to the 
plasma membrane called the cell wall. The cell wall is a rigid covering that 
protects the cell, provides structural support, and gives shape to the cell. 
Fungal and protist cells also have cell walls. 


While the chief component of prokaryotic cell walls is peptidoglycan, the 
major organic molecule in the plant cell wall is cellulose, a polysaccharide 
made up of long, straight chains of glucose units. When nutritional 
information refers to dietary fiber, it is referring to the cellulose content of 
food. 


Chloroplasts 


Like mitochondria, chloroplasts also have their own DNA and ribosomes. 
Chloroplasts function in photosynthesis and can be found in eukaryotic 
cells such as plants and algae. In photosynthesis, carbon dioxide, water, and 
light energy are used to make glucose and oxygen. This is the major 
difference between plants and animals: Plants (autotrophs) are able to make 
their own food, like glucose, whereas animals (heterotrophs) must rely on 
other organisms for their organic compounds or food source. 


Intermembrane Outer 
space membrane 


Inner 
membrane 


Granum 
(stack of 
thylakoids) 


Stroma 
Thylakoid (aqueous fluid) 


This simplified diagram of a 

chloroplast shows the outer 
membrane, inner membrane, 
thylakoids, grana, and stroma. 


The chloroplasts contain a green pigment called chlorophyll, which 
captures the energy of sunlight for photosynthesis. Like plant cells, 
photosynthetic protists also have chloroplasts. Some bacteria also perform 
photosynthesis, but they do not have chloroplasts. Their photosynthetic 
pigments are located in the thylakoid membrane within the cell itself. 


Section Summary 


Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, 
cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a 
prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a 
membrane), and has other membrane-bound organelles that allow for 
compartmentalization of functions. The plasma membrane is a phospholipid 
bilayer embedded with proteins. Mitochondria perform cellular respiration 
and produce ATP. 


Plant cells have a cell wall, chloroplasts, and a central vacuole. The plant 
cell wall, whose primary component is cellulose, protects the cell, provides 


structural support, and gives shape to the cell. Photosynthesis takes place in 
chloroplasts. 


Glossary 


cell wall 
a rigid cell covering made of cellulose in plants, peptidoglycan in 
bacteria, non-peptidoglycan compounds in Archaea, and chitin in fungi 
that protects the cell, provides structural support, and gives shape to 
the cell 


central vacuole 
a large plant cell organelle that acts as a storage compartment, water 
reservoir, and site of macromolecule degradation 


chloroplast 
a plant cell organelle that carries out photosynthesis 


cilium 
(plural: cilia) a short, hair-like structure that extends from the plasma 
membrane in large numbers and is used to move an entire cell or move 
substances along the outer surface of the cell 


cytoplasm 
the entire region between the plasma membrane and the nuclear 
envelope, consisting of organelles suspended in the gel-like cytosol, 
the cytoskeleton, and various chemicals 


cytoskeleton 
the network of protein fibers that collectively maintains the shape of 
the cell, secures some organelles in specific positions, allows 
cytoplasm and vesicles to move within the cell, and enables unicellular 
organisms to move 


cytosol 
the gel-like material of the cytoplasm in which cell structures are 
suspended 


desmosome 
a linkage between adjacent epithelial cells that forms when cadherins 
in the plasma membrane attach to intermediate filaments 


endomembrane system 
the group of organelles and membranes in eukaryotic cells that work 
together to modify, package, and transport lipids and proteins 


endoplasmic reticulum (ER) 
a series of interconnected membranous structures within eukaryotic 
cells that collectively modify proteins and synthesize lipids 


extracellular matrix 
the material, primarily collagen, glycoproteins, and proteoglycans, 
secreted from animal cells that holds cells together as a tissue, allows 
cells to communicate with each other, and provides mechanical 
protection and anchoring for cells in the tissue 


flagellum 
(plural: flagella) the long, hair-like structure that extends from the 
plasma membrane and is used to move the cell 


gap junction 
a channel between two adjacent animal cells that allows ions, 
nutrients, and other low-molecular weight substances to pass between 
the cells, enabling the cells to communicate 


Golgi apparatus 
a eukaryotic organelle made up of a series of stacked membranes that 
sorts, tags, and packages lipids and proteins for distribution 


lysosome 
an organelle in an animal cell that functions as the cell’s digestive 
component; it breaks down proteins, polysaccharides, lipids, nucleic 
acids, and even worn-out organelles 


mitochondria 


(singular: mitochondrion) the cellular organelles responsible for 
carrying out cellular respiration, resulting in the production of ATP, the 
cell’s main energy-carrying molecule 


nuclear envelope 
the double-membrane structure that constitutes the outermost portion 
of the nucleus 


nucleolus 
the darkly staining body within the nucleus that is responsible for 
assembling ribosomal subunits 


nucleus 
the cell organelle that houses the cell’s DNA and directs the synthesis 
of ribosomes and proteins 


peroxisome 
a small, round organelle that contains hydrogen peroxide, oxidizes 
fatty acids and amino acids, and detoxifies many poisons 


plasma membrane 
a phospholipid bilayer with embedded (integral) or attached 
(peripheral) proteins that separates the internal contents of the cell 
from its surrounding environment 


plasmodesma 
(plural: plasmodesmata) a channel that passes between the cell walls of 
adjacent plant cells, connects their cytoplasm, and allows materials to 
be transported from cell to cell 


ribosome 
a cellular structure that carries out protein synthesis 


rough endoplasmic reticulum (RER) 
the region of the endoplasmic reticulum that is studded with ribosomes 


and engages in protein modification 


smooth endoplasmic reticulum (SER) 


the region of the endoplasmic reticulum that has few or no ribosomes 
on its cytoplasmic surface and synthesizes carbohydrates, lipids, and 
steroid hormones; detoxifies chemicals like pesticides, preservatives, 
medications, and environmental pollutants, and stores calcium ions 


tight junction 
a firm seal between two adjacent animal cells created by protein 
adherence 


vacuole 
a membrane-bound sac, somewhat larger than a vesicle, that functions 
in cellular storage and transport 


vesicle 
a small, membrane-bound sac that functions in cellular storage and 
transport; its membrane is capable of fusing with the plasma 
membrane and the membranes of the endoplasmic reticulum and Golgi 
apparatus 


The Cell Membrane EnBio 
By the end of this section, you will be able to: 


e Understand the fluid mosaic model of membranes 


A cell’s plasma membrane defines the boundary of the cell and determines 
the nature of its contact with the environment. Cells exclude some 
substances, take in others, and excrete still others, all in controlled 
quantities. Plasma membranes enclose the borders of cells, but rather than 
being a static bag, they are dynamic and constantly in flux. 


Fluid Mosaic Model 


In 1972, S. J. Singer and Garth L. Nicolson proposed a new model of the 
plasma membrane that, compared to earlier understanding, better explained 
both microscopic observations and the function of the plasma membrane. 
This was called the fluid mosaic model. The model has evolved somewhat 
over time, but still best accounts for the structure and functions of the 
plasma membrane as we now understand them. The fluid mosaic model 
describes the structure of the plasma membrane as a mosaic of components 
—including phospholipids, cholesterol, proteins, and carbohydrates—in 
which the components are able to flow and change position, while 
maintaining the basic integrity of the membrane. 


Glycoprotein: protein with Glycolipid: lipid with 
| ra carbohydrate 
attached 


carbohydrate attached 


Peripheral membrane Phospholipid 


Prom bilayer 
Integral membrane Cholesterol : 
protein Protein channel 


Filaments of the cytoskeleton 


The fluid mosaic model of the plasma membrane 


structure describes the plasma membrane as a fluid 
combination of phospholipids, cholesterol, 
proteins, and carbohydrates. 


The plasma membrane is made up primarily of a bilayer of phospholipids 
with embedded proteins, carbohydrates, glycolipids, and glycoproteins, and, 
in animal cells, cholesterol. The amount of cholesterol in animal plasma 
membranes regulates the fluidity of the membrane and changes based on 
the temperature of the cell’s environment. In other words, cholesterol acts 
as antifreeze in the cell membrane and is more abundant in animals that live 
in cold climates. 


The main fabric of the membrane is composed of two layers of 
phospholipid molecules, and the polar ends of these molecules (which look 
like a collection of balls in an artist’s rendition of the model) ({link]) are in 
contact with aqueous fluid both inside and outside the cell. Thus, both 
surfaces of the plasma membrane are hydrophilic. In contrast, the interior of 
the membrane, between its two surfaces, is a hydrophobic or nonpolar 
region because of the fatty acid tails. This region has no attraction for water 
or other polar molecules. 


Glossary 


fluid mosaic model 
a model of the structure of the plasma membrane as a mosaic of 
components, including phospholipids, cholesterol, proteins, and 
glycolipids, resulting in a fluid rather than static character 


Passive Transport EnBio 
By the end of this section, you will be able to: 


e Explain why and how passive transport occurs 
e Understand the processes of osmosis and diffusion 
e Define tonicity and describe its relevance to passive transport 


Plasma membranes must allow certain substances to enter and leave a cell, 
while preventing harmful material from entering and essential material from 
leaving. In other words, plasma membranes are selectively permeable— 
they allow some substances through but not others. If they were to lose this 
selectivity, the cell would no longer be able to sustain itself, and it would be 
destroyed. Some cells require larger amounts of specific substances than do 
other cells; they must have a way of obtaining these materials from the 
extracellular fluids. This may happen passively, as certain materials move 
back and forth, or the cell may have special mechanisms that ensure 
transport. 


The most direct forms of membrane transport are passive. Passive 
transport is a naturally occurring phenomenon and does not require the cell 
to expend energy to accomplish the movement. In passive transport, 
substances move from an area of higher concentration to an area of lower 
concentration in a process called diffusion. A physical space in which there 
is a different concentration of a single substance is said to have a 
concentration gradient. 


Diffusion 


Diffusion is a passive process of transport. A single substance tends to 
move from an area of high concentration to an area of low concentration 
until the concentration is equal across the space. You are familiar with 
diffusion of substances through the air. For example, think about someone 
opening a bottle of perfume in a room filled with people. The perfume is at 
its highest concentration in the bottle and is at its lowest at the edges of the 
room. The perfume vapor will diffuse, or spread away, from the bottle, and 
gradually, more and more people will smell the perfume as it spreads. 
Materials move within the cell’s cytosol by diffusion, and certain materials 


move through the plasma membrane by diffusion ([link]). Diffusion 
expends no energy. Rather the different concentrations of materials in 
different areas are a form of potential energy, and diffusion is the 
dissipation of that potential energy as materials move down their 
concentration gradients, from high to low. 


Lipid bilayer 
(plasma { 
membrane) 


TIME 


Diffusion through a permeable membrane follows the 
concentration gradient of a substance, moving the 
substance from an area of high concentration to one 
of low concentration. (credit: modification of work by 
Mariana Ruiz Villarreal) 


Note: 
Concept in Action 


= 
mess Openstax COLLEGE 


For an animation of the diffusion process in action, view this short video 
on cell membrane transport. 


Osmosis 


Osmosis is the diffusion of water through a semipermeable membrane 
according to the concentration gradient of water across the membrane. 
Whereas diffusion transports material across membranes and within cells, 
osmosis transports only water across a membrane and the membrane limits 
the diffusion of solutes in the water. Osmosis is a special case of diffusion. 
Water, like other substances, moves from an area of higher concentration to 
one of lower concentration. Imagine a beaker with a semipermeable 
membrane, separating the two sides or halves ({link]). On both sides of the 
membrane, the water level is the same, but there are different 
concentrations on each side of a dissolved substance, or solute, that cannot 
cross the membrane. If the volume of the water is the same, but the 
concentrations of solute are different, then there are also different 
concentrations of water, the solvent, on either side of the membrane. 


Semipermeable membrane 


In osmosis, water always moves from an 
area of higher concentration (of water) to 
one of lower concentration (of water). In this 


system, the solute cannot pass through the 
selectively permeable membrane. 


A principle of diffusion is that the molecules move around and will spread 
evenly throughout the medium if they can. However, only the material 
capable of getting through the membrane will diffuse through it. In this 
example, the solute cannot diffuse through the membrane, but the water 
can. Water has a concentration gradient in this system. Therefore, water will 
diffuse down its concentration gradient, crossing the membrane to the side 
where it is less concentrated. This diffusion of water through the membrane 
—osmosis—will continue until the concentration gradient of water goes to 
zero. Osmosis proceeds constantly in living systems. 


Note: 
Concept in Action 


He 


— Je COLLEGE” 


Watch this video that illustrates diffusion in hot versus cold solutions. 


Section Summary 


The passive forms of transport, diffusion and osmosis, move material of 
small molecular weight. Substances diffuse from areas of high 
concentration to areas of low concentration, and this process continues until 
the substance is evenly distributed in a system. In solutions of more than 
one substance, each type of molecule diffuses according to its own 
concentration gradient. Many factors can affect the rate of diffusion, 


including concentration gradient, the sizes of the particles that are diffusing, 
and the temperature of the system. 


In living systems, diffusion of substances into and out of cells is mediated 
by the plasma membrane. Some materials diffuse readily through the 
membrane, but others are hindered, and their passage is only made possible 
by protein channels and carriers. The chemistry of living things occurs in 
aqueous solutions, and balancing the concentrations of those solutions is an 
ongoing problem. In living systems, diffusion of some substances would be 
slow or difficult without membrane proteins. 


Glossary 


concentration gradient 
an area of high concentration across from an area of low concentration 


diffusion 
a passive process of transport of low-molecular weight material down 
its concentration gradient 


facilitated transport 
a process by which material moves down a concentration gradient 
(from high to low concentration) using integral membrane proteins 


hypertonic 
describes a solution in which extracellular fluid has higher osmolarity 
than the fluid inside the cell 


hypotonic 
describes a solution in which extracellular fluid has lower osmolarity 
than the fluid inside the cell 


isotonic 
describes a solution in which the extracellular fluid has the same 
osmolarity as the fluid inside the cell 


osmolarity 


the total amount of substances dissolved in a specific amount of 
solution 


osmosis 
the transport of water through a semipermeable membrane from an 
area of high water concentration to an area of low water concentration 
across a membrane 


passive transport 
a method of transporting material that does not require energy 


selectively permeable 
the characteristic of a membrane that allows some substances through 
but not others 


solute 
a substance dissolved in another to form a solution 


tonicity 
the amount of solute in a solution. 


Introduction Obtain Energy EnBio 
class="introduction" 


A 
hummingbir 
d needs 
energy to 
maintain 
prolonged 
flight. The 
bird obtains 
its energy 
from taking 
in food and 
transforming 
the energy 
contained in 
food 
molecules 
into forms of 
energy to 
power its 
flight 
through a 
series of 
biochemical 
reactions. 
(credit: 
modification 
of work by 
Cory 
Zanker) 


Virtually every task performed by living organisms requires energy. Energy 
is needed to perform heavy labor and exercise, but humans also use energy 
while thinking, and even during sleep. In fact, the living cells of every 
organism constantly use energy. Nutrients and other molecules are imported 
into the cell, metabolized (broken down) and possibly synthesized into new 
molecules, modified if needed, transported around the cell, and possibly 
distributed to the entire organism. For example, the large proteins that make 
up muscles are built from smaller molecules imported from dietary amino 
acids. Complex carbohydrates are broken down into simple sugars that the 
cell uses for energy. Just as energy is required to both build and demolish a 
building, energy is required for the synthesis and breakdown of molecules 
as well as the transport of molecules into and out of cells. In addition, 
processes such as ingesting and breaking down pathogenic bacteria and 
viruses, exporting wastes and toxins, and movement of the cell require 
energy. How do living cells obtain energy, and how do they use it? This 
chapter will discuss different forms of energy and the physical laws that 
govern energy transfer. 


Energy and Metabolism EnBio 
By the end of this section, you will be able to: 


e Explain what metabolic pathways are 

State the first and second laws of thermodynamics 

e Explain the difference between kinetic and potential energy 
Describe endergonic and exergonic reactions 

e Discuss how enzymes function as molecular catalysts 


Scientists use the term bioenergetics to describe the concept of energy flow 
({link]) through living systems, such as cells. Cellular processes such as the 
building and breaking down of complex molecules occur through stepwise 
chemical reactions. Some of these chemical reactions are spontaneous and 
release energy, whereas others require energy to proceed. Just as living 
things must continually consume food to replenish their energy supplies, 
cells must continually obtain more energy to replenish that used by the 
many energy-requiring chemical reactions that constantly take place. 
Together, all of the chemical reactions that take place inside cells, including 
those that consume or generate energy, are referred to as the cell’s 
metabolism. 


23 


— 
os 
=m 


Ultimately, most life forms get their 
energy from the sun. Plants use 
photosynthesis to capture sunlight, 
and herbivores eat the plants to obtain 
energy. Carnivores eat the herbivores, 
and eventual decomposition of plant 
and animal material contributes to the 
nutrient pool. 


Metabolic Pathways 


Consider the metabolism of sugar. This is a classic example of one of the 
many cellular processes that use and produce energy. Living things 
consume sugars as a major energy source, because sugar molecules have a 
great deal of energy stored within their bonds. For the most part, 
photosynthesizing organisms like plants produce these sugars. During 
photosynthesis, plants use energy (originally from sunlight) to convert 
carbon dioxide gas (CO>) into sugar molecules (like glucose: CgH 0g). 
They consume carbon dioxide and produce oxygen as a waste product. This 
reaction is summarized as: 

Equation: 


6CO, + 6H,0 --> CHO. + 60, 


Because this process involves synthesizing an energy-storing molecule, it 
requires energy input to proceed. During the light reactions of 
photosynthesis, energy is provided by a molecule called adenosine 
triphosphate (ATP), which is the primary energy currency of all cells. Just 
as the dollar is used as currency to buy goods, cells use molecules of ATP 
as energy currency to perform immediate work. In contrast, energy-storage 
molecules such as glucose are consumed only to be broken down to use 
their energy. The reaction that harvests the energy of a sugar molecule in 
cells requiring oxygen to survive can be summarized by the reverse reaction 


to photosynthesis. In this reaction, oxygen is consumed and carbon dioxide 
is released as a waste product. The reaction is summarized as: 
Equation: 


CoH,.0, + 60, --> 6H,O + 6CO, 


Both of these reactions involve many steps. 


The processes of making and breaking down sugar molecules illustrate two 
examples of metabolic pathways. A metabolic pathway is a series of 
chemical reactions that takes a starting molecule and modifies it, step-by- 
step, through a series of metabolic intermediates, eventually yielding a final 
product. In the example of sugar metabolism, the first metabolic pathway 
synthesized sugar from smaller molecules, and the other pathway broke 
sugar down into smaller molecules. These two opposite processes—the first 
requiring energy and the second producing energy—are referred to as 
anabolic pathways (building polymers) and catabolic pathways (breaking 
down polymers into their monomers), respectively. Consequently, 
metabolism is composed of synthesis (anabolism) and degradation 
(catabolism) ({link]). 


It is important to know that the chemical reactions of metabolic pathways 
do not take place on their own. Each reaction step is facilitated, or 
catalyzed, by a protein called an enzyme. Enzymes are important for 
catalyzing all types of biological reactions—those that require energy as 
well as those that release energy. 


Metabolic pathways 


Anabolic: Small molecules are built into large ones. Energy is required. 


oeeo = 0000 


Catabolic: Large molecules are broken down into small ones. Energy is released. 


©0008 — © © © O 


Catabolic pathways are those that generate energy by breaking 
down larger molecules. Anabolic pathways are those that 
require energy to synthesize larger molecules. Both types of 
pathways are required for maintaining the cell’s energy 
balance. 


Energy 


Thermodynamics refers to the study of energy and energy transfer 
involving physical matter. The matter relevant to a particular case of energy 
transfer is called a system, and everything outside of that matter is called 
the surroundings. For instance, when heating a pot of water on the stove, 
the system includes the stove, the pot, and the water. Energy is transferred 
within the system (between the stove, pot, and water). There are two types 
of systems: open and closed. In an open system, energy can be exchanged 
with its surroundings. The stovetop system is open because heat can be lost 
to the air. A closed system cannot exchange energy with its surroundings. 


Biological organisms are open systems. Energy is exchanged between them 
and their surroundings as they use energy from the sun to perform 
photosynthesis or consume energy-storing molecules and release energy to 
the environment by doing work and releasing heat. Like all things in the 
physical world, energy is subject to physical laws. The laws of 
thermodynamics govern the transfer of energy in and among all systems in 
the universe. 


In general, energy is defined as the ability to do work, or to create some 
kind of change. Energy exists in different forms. For example, electrical 
energy, light energy, and heat energy are all different types of energy. To 
appreciate the way energy flows into and out of biological systems, it is 
important to understand two of the physical laws that govern energy. 


Thermodynamics 


The first law of thermodynamics states that the total amount of energy in 
the universe is constant and conserved. In other words, there has always 
been, and always will be, exactly the same amount of energy in the 
universe. Energy exists in many different forms. According to the first law 
of thermodynamics, energy may be transferred from place to place or 
transformed into different forms, but it cannot be created or destroyed. The 
transfers and transformations of energy take place around us all the time. 
Light bulbs transform electrical energy into light and heat energy. Gas 
stoves transform chemical energy from natural gas into heat energy. Plants 
perform one of the most biologically useful energy transformations on 
earth: that of converting the energy of sunlight to chemical energy stored 
within organic molecules ([link]). Some examples of energy 
transformations are shown in [link]. 


The challenge for all living organisms is to obtain energy from their 
surroundings in forms that they can transfer or transform into usable energy 
to do work. Living cells have evolved to meet this challenge. Chemical 
energy stored within organic molecules such as sugars and fats is 
transferred and transformed through a series of cellular chemical reactions 
into energy within molecules of ATP. Energy in ATP molecules is easily 
accessible to do work. Examples of the types of work that cells need to do 
include building complex molecules, transporting materials, powering the 
motion of cilia or flagella, and contracting muscle fibers to create 
movement. 


Chemical energy Light energy 


od od 


Kinetic energy Chemical energy 


Shown are some examples of energy 
transferred and transformed from one 
system to another and from one form to 
another. The food we consume provides our 
cells with the energy required to carry out 
bodily functions, just as light energy 
provides plants with the means to create the 
chemical energy they need. (credit "ice 
cream": modification of work by D. Sharon 
Pruitt; credit "kids": modification of work 
by Max from Providence; credit "leaf": 
modification of work by Cory Zanker) 


A living cell’s primary tasks of obtaining, transforming, and using energy to 
do work may seem simple. However, the second law of thermodynamics 
explains why these tasks are harder than they appear. All energy transfers 
and transformations are never completely efficient. In every energy transfer, 
some amount of energy is lost in a form that is unusable. In most cases, this 
form is heat energy. Thermodynamically, heat energy is defined as the 
energy transferred from one system to another that is not work. For 
example, when a light bulb is turned on, some of the energy being 
converted from electrical energy into light energy is lost as heat energy. 
Likewise, some energy is lost as heat energy during cellular metabolic 
reactions. 


Potential and Kinetic Energy 


When an object is in motion, there is energy associated with that object. 
Think of a wrecking ball. Even a slow-moving wrecking ball can do a great 
deal of damage to other objects. Energy associated with objects in motion is 
called kinetic energy ((link]). A speeding bullet, a walking person, and the 
rapid movement of molecules in the air (which produces heat) all have 
kinetic energy. 


Now what if that same motionless wrecking ball is lifted two stories above 
ground with a crane? If the suspended wrecking ball is unmoving, is there 
energy associated with it? The answer is yes. The energy that was required 
to lift the wrecking ball did not disappear, but is now stored in the wrecking 
ball by virtue of its position and the force of gravity acting on it. This type 
of energy is called potential energy ((link]). If the ball were to fall, the 
potential energy would be transformed into kinetic energy until all of the 
potential energy was exhausted when the ball rested on the ground. 


is 


Still water has potential energy; moving water, such as in 
a waterfall or a rapidly flowing river, has kinetic energy. 
(credit "dam": modification of work by "Pascal"/Flickr; 
credit "waterfall": modification of work by Frank 
Gualtieri) 


Potential energy is not only associated with the location of matter, but also 
with the structure of matter. Even a spring on the ground has potential 
energy if it is compressed; so does a rubber band that is pulled taut. On a 
molecular level, the bonds that hold the atoms of molecules together exist in 
a particular structure that has potential energy. Remember that anabolic 
cellular pathways require energy to synthesize complex molecules from 
simpler ones and catabolic pathways release energy when complex 
molecules are broken down. The fact that energy can be released by the 
breakdown of certain chemical bonds implies that those bonds have 
potential energy. In fact, there is potential energy stored within the bonds of 
all the food molecules we eat, which is eventually harnessed for use. This is 
because these bonds can release energy when broken. The type of potential 
energy that exists within chemical bonds, and is released when those bonds 
are broken, is called chemical energy. Chemical energy is responsible for 
providing living cells with energy from food. The release of energy occurs 
when the molecular bonds within food molecules are broken. 


Note: 
Concept in Action 


Obra 


Visit the site and select “Pendulum” from the “Work and Energy” menu to 
see the shifting kinetic and potential energy of a pendulum in motion. 


Enzymes 


A substance that helps a chemical reaction to occur is called a catalyst, and 
the molecules that catalyze biochemical reactions are called enzymes. Most 
enzymes are proteins. Most of the reactions critical to a living cell happen 
too slowly at normal temperatures to be of any use to the cell. Without 
enzymes to speed up these reactions, life could not persist. In addition, an 
enzyme itself is unchanged by the reaction it catalyzes. Once one reaction 
has been catalyzed, the enzyme is able to participate in other reactions. The 
chemical reactants to which an enzyme binds are called the enzyme’s 
substrates. There may be one or more substrates, depending on the 
particular chemical reaction. Enzymes can also be regulated in ways that 
either promote or reduce enzyme activity. There are many kinds of 
molecules that inhibit or promote enzyme function, and various 
mechanisms by which they do so. 


Many enzymes do not work optimally, or even at all, unless bound to other 
specific non-protein helper molecules. They may bond either temporarily 
through ionic or hydrogen bonds, or permanently through stronger covalent 
bonds. Binding to these molecules promotes optimal shape and function of 
their respective enzymes. Two examples of these types of helper molecules 
are cofactors and coenzymes. Cofactors are inorganic ions such as ions of 
iron and magnesium. Coenzymes are organic helper molecules, those with a 


basic atomic structure made up of carbon and hydrogen. Like enzymes, 
these molecules participate in reactions without being changed themselves 
and are ultimately recycled and reused. Vitamins are the source of 
coenzymes. Some vitamins are the precursors of coenzymes and others act 
directly as coenzymes. Vitamin C is a direct coenzyme for multiple 
enzymes that take part in building the important connective tissue, collagen. 
Therefore, enzyme function is, in part, regulated by the abundance of 
various cofactors and coenzymes, which may be supplied by an organism’s 
diet or, in some cases, produced by the organism. 


Section Summary 


Cells perform the functions of life through various chemical reactions. A 
cell’s metabolism refers to the combination of chemical reactions that take 
place within it. Catabolic reactions break down complex chemicals into 
simpler ones and are associated with energy release. Anabolic processes 
build complex molecules out of simpler ones and require energy. 


In studying energy, the term system refers to the matter and environment 
involved in energy transfers. Entropy is a measure of the disorder of a 
system. The physical laws that describe the transfer of energy are the laws 
of thermodynamics. The first law states that the total amount of energy in 
the universe is constant. The second law of thermodynamics states that 
every energy transfer involves some loss of energy in an unusable form, 
such as heat energy. Energy comes in different forms: kinetic, potential, and 
free. The change in free energy of a reaction can be negative (releases 
energy, exergonic) or positive (consumes energy, endergonic). All reactions 
require an initial input of energy to proceed, called the activation energy. 


Enzymes are chemical catalysts that speed up chemical reactions. Chemical 
reactants for an enzyme are called substrates. Enzyme action is regulated to 
conserve resources and respond optimally to the environment. 


Glossary 


activation energy 
the amount of initial energy necessary for reactions to occur 


active site 
a specific region on the enzyme where the substrate binds 


allosteric inhibition 
the mechanism for inhibiting enzyme action in which a regulatory 
molecule binds to a second site (not the active site) and initiates a 
conformation change in the active site, preventing binding with the 
substrate 


anabolic 
describes the pathway that requires a net energy input to synthesize 
complex molecules from simpler ones 


bioenergetics 
the concept of energy flow through living systems 


catabolic 
describes the pathway in which complex molecules are broken down 
into simpler ones, yielding energy as an additional product of the 
reaction 


competitive inhibition 
a general mechanism of enzyme activity regulation in which a 
molecule other than the enzyme’s substrate is able to bind the active 
site and prevent the substrate itself from binding, thus inhibiting the 
overall rate of reaction for the enzyme 


endergonic 
describes a chemical reaction that results in products that store more 
chemical potential energy than the reactants 


enzyme 
a molecule that catalyzes a biochemical reaction 


exergonic 
describes a chemical reaction that results in products with less 
chemical potential energy than the reactants, plus the release of free 
energy 


feedback inhibition 
a mechanism of enzyme activity regulation in which the product of a 
reaction or the final product of a series of sequential reactions inhibits 
an enzyme for an earlier step in the reaction series 


heat energy 
the energy transferred from one system to another that is not work 


kinetic energy 
the type of energy associated with objects in motion 


metabolism 
all the chemical reactions that take place inside cells, including those 
that use energy and those that release energy 


noncompetitive inhibition 
a general mechanism of enzyme activity regulation in which a 
regulatory molecule binds to a site other than the active site and 
prevents the active site from binding the substrate; thus, the inhibitor 
molecule does not compete with the substrate for the active site; 
allosteric inhibition is a form of noncompetitive inhibition 


potential energy 
the type of energy that refers to the potential to do work 


substrate 
a molecule on which the enzyme acts 


thermodynamics 
the science of the relationships between heat, energy, and work 


Fermentation EnBio 
By the end of this section, you will be able to: 


e Discuss the fundamental difference between anaerobic cellular 
respiration and fermentation 

e Describe the type of fermentation that readily occurs in animal cells 
and the conditions that initiate that fermentation 


In aerobic respiration, the final electron acceptor is an oxygen molecule, O>. 
If aerobic respiration occurs, then ATP will be produced using the energy of 
the high-energy electrons carried by NADH or FADH+> to the electron 
transport chain. Some living systems use an organic molecule as the final 
electron acceptor. Processes that use an organic molecule to regenerate 
NAD* from NADH are collectively referred to as fermentation. In 
contrast, some living systems use an inorganic molecule as a final electron 
acceptor; both methods are a type of anaerobic cellular respiration. 
Anaerobic respiration enables organisms to convert energy for their use in 
the absence of oxygen. 


Lactic Acid Fermentation 


The fermentation method used by animals and some bacteria like those in 
yogurt is lactic acid fermentation ({link]). This occurs routinely in 
mammalian red blood cells and in skeletal muscle that has insufficient 
oxygen supply to allow aerobic respiration to continue (that is, in muscles 
used to the point of fatigue). In muscles, lactic acid produced by 
fermentation must be removed by the blood circulation and brought to the 
liver for further metabolism. The chemical reaction of lactic acid 
fermentation is the following: 

Equation: 


Pyruvic acid + NADH + lactic acid + NAD* 


Note: 


Art Connection 


Lactic Acid Fermentation 


2 Pyruvate 


2 Lactate 


i= 
2 
# 
oD 
I 
od 
iv 


Lactic acid fermentation is 
common in muscles that have 
become exhausted by use. 


Alcohol Fermentation 


Another familiar fermentation process is alcohol fermentation ({link]), 
which produces ethanol, an alcohol. The alcohol fermentation reaction is 
the following: 


Pyruvic acid ———_—» CO, + Acetaldehyde 


Acetaldehyde Ethanol 


NADH NAD* 


The reaction resulting in alcohol 
fermentation is shown. 


In the first reaction, a carboxyl group is removed from pyruvic acid, 
releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the 
molecule by one carbon atom, making acetaldehyde. The second reaction 
removes an electron from NADH, forming NAD* and producing ethanol 
from the acetaldehyde, which accepts the electron. The fermentation of 
pyruvic acid by yeast produces the ethanol found in alcoholic beverages 
({link]). If the carbon dioxide produced by the reaction is not vented from 
the fermentation chamber, for example in beer and sparkling wines, it 
remains dissolved in the medium until the pressure is released. Ethanol 
above 12 percent is toxic to yeast, so natural levels of alcohol in wine occur 
at a maximum of 12 percent. 


Fermentation of grape juice to 
make wine produces CO) as a 
byproduct. Fermentation tanks 
have valves so that pressure 
inside the tanks can be released. 


Anaerobic Cellular Respiration 


Certain prokaryotes, including some species of bacteria and Archaea, use 
anaerobic respiration. For example, the group of Archaea called 
methanogens reduces carbon dioxide to methane to oxidize NADH. These 
microorganisms are found in soil and in the digestive tracts of ruminants, 
such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea, 
most of which are anaerobic ({link]), reduce sulfate to hydrogen sulfide to 
regenerate NAD” from NADH. 


The green color seen in these coastal waters is 


from an eruption of hydrogen sulfide. Anaerobic, 

sulfate-reducing bacteria release hydrogen sulfide 

gas as they decompose algae in the water. (credit: 
NASA image courtesy Jeff Schmaltz, MODIS 
Land Rapid Response Team at NASA GSFC) 


Note: 
Concept in Action 


mayen 


meee, OPENStAX COLLEGE 
. 
f=) 

rh 


Visit this site to see anaerobic cellular respiration in action. 


Other fermentation methods occur in bacteria. Many prokaryotes are 
facultatively anaerobic. This means that they can switch between aerobic 
respiration and fermentation, depending on the availability of oxygen. 
Certain prokaryotes, like Clostridia bacteria, are obligate anaerobes. 
Obligate anaerobes live and grow in the absence of molecular oxygen. 
Oxygen is a poison to these microorganisms and kills them upon exposure. 


Section Summary 


If NADH cannot be metabolized through aerobic respiration, another 
electron acceptor is used. Most organisms will use some form of 
fermentation to accomplish the regeneration of NAD", ensuring the 
continuation of glycolysis. 


Glossary 


anaerobic cellular respiration 
the use of an electron acceptor other than oxygen to complete 
metabolism using electron transport-based chemiosmosis 


fermentation 
the steps that follow the partial oxidation of glucose via glycolysis to 
regenerate NAD*; occurs in the absence of oxygen and uses an organic 
compound as the final electron acceptor 


Introduction Photosynthesis EnBio 
class="introduction" 


This sage 
thrasher’s diet, 
like that of 
almost all 
organisms, 
depends on 
photosynthesis 
. (credit: 
modification 
of work by 
Dave Menke, 
U.S. Fish and 
Wildlife 
Service) 


No matter how complex or advanced a machine, such as the latest cellular 
phone, the device cannot function without energy. Living things, similar to 
machines, have many complex components; they too cannot do anything 
without energy, which is why humans and all other organisms must “eat” in 


some form or another. That may be common knowledge, but how many 
people realize that every bite of every meal ingested depends on the process 
of photosynthesis? 


Appendix EnBio 


Periodic Table of the Elements 


Grou 
iM Pp 


1 
i] 
101 
Hydrogen 2 


Periodic Table of the Elements 


= 


N 


Ar 


Bie] 9 2 


Spas 
AB AAA EERE RIE 


i 81 
132.9 204.4 
Thallium 


ae “Bs 
Fr “Rg ‘Dut 
[223] es, (Bs olga 1 p24 
Francium: pruners 


—- 


Atomic Other non-metals 
Number L) : 
Symbol [1] Alkali metals 
Relative {_ | Transition metals 
Name Hydrogen Atomic Mass [_] Other metals 


{_] Alkaline earth metals 
|_| Halogens 


Measurements and the Metric System 


Measurements and the Metric System 


{| Noble gases 
{_] Lanthanides 
[_] Actinides 


[_] Unknown 
chemical 
properties 


Measurement Unit Abbreviation 
Length 
nanometer nm 
micrometer pm 


Metric 
Equivalent 


1lnm= 
10°°m 


1 pm = 
10°°m 


Approximate 
Standard 
Equivalent 


e 1mm= 
0.039 
inch 

e lcm= 
0.394 


: inch 
Measurements and the Metric System 


e lm= 
Approximate 
Metric Standard_ 
Measurement Unit Abbreviation Equivalent Equiy nt 
1mm = pees 
millimeter mm 0.001 m 1.093 
yards 
nee e 1km= 
centimeter cm ee 0.621 
0.01 m 
miles 
e 1lm= 
100 
cm 
meter m 
e lm= 
1000 
mm 
; 1km= 
kilometer km 1000 m 
1 pg = 10° 
microgram pg P 
: * 1g= 
milligram mg ' of ~ 0.035 
8 ounce 
Mass © 1kg= 
gram g Pere 2.205 
mg 
pounds 
: 1kg= 
kilogram kg 1000 g 
Volume 2 it ipk=10-° 
microliter pl 1 6 Gare 
0.034 
ae! 1 ml = 10° fluid 
milliliter ml I ae 
e 11= 
= 1.057 
liter l pe ee 


ml quarts 


Measurements and the Metric System 


Measurement 


Area 


Temperature 


Unit 


kiloliter 


square 
centimeter 


square 
meter 


hectare 


Celsius 


Abbreviation 


kl 


cm 


ha 


ad @ 


Metric 
Equivalent 


1 kl = 1000 
l 


1 cm2 = 
100 mm? 


1 m2 = 
10,000 cm? 


1 ha= 
10,000 m2 


Approximate 
Standard 
Equivalent 


e 1kl= 
264.172 
gallons 


0.155 
square 
inch 


° 1m= 
10.764 
square 
feet 


square 
yards 
e tha= 
2.471 
acres 


1°G=5/9* 
(°F — 32) 


ATP EnBio 
By the end of this section, you will be able to: 


e Explain how ATP is used by the cell as an energy source 


Within the cell, where does energy to power chemical reactions come from? 
The answer lies with an energy-supplying molecule called adenosine 
triphosphate, or ATP. ATP is a small, relatively simple molecule, but within 
its bonds contains the potential for a quick burst of energy that can be 
harnessed to perform cellular work. This molecule can be thought of as the 
primary energy currency of cells in the same way that money is the 
currency that people exchange for things they need. ATP is used to power 
the majority of energy-requiring cellular reactions. 


ATP in Living Systems 


When ATP is broken down, usually by the removal of its terminal 
phosphate group, energy is released. This energy is used to do work by the 
cell, usually by the binding of the released phosphate to another molecule, 
thus activating it. For example, in the mechanical work of muscle 
contraction, ATP supplies energy to move the contractile muscle proteins. 


ATP Structure and Function 


At the heart of ATP is a molecule of adenosine monophosphate (AMP), 
which is composed of an adenine molecule bonded to both a ribose 
molecule and a single phosphate group ([link]). Ribose is a five-carbon 
sugar found in RNA and AMP is one of the nucleotides in RNA. The 
addition of a second phosphate group to this core molecule results in 
adenosine diphosphate (ADP); the addition of a third phosphate group 
forms adenosine triphosphate (ATP). The release of one or two phosphate 
groups from ATP, a process called hydrolysis, releases energy. 


HoN 


Gamma Alpha 
phosphate phosphate — N 
group group N 
fe) fe) fe) ll \ » 
_ il II I| N 
i : i Y ji = O " Adenine 
O- Oo” on 
Beta 
phosphate OH OH 
group 7 
Ribose 


The structure of ATP shows the basic 
components of a two-ring adenine, five- 
carbon ribose, and three phosphate 
groups. 


Section Summary 


ATP functions as the energy currency for cells. It allows cells to store 
energy briefly and transport it within itself to support endergonic chemical 
reactions. The structure of ATP is that of an RNA nucleotide with three 
phosphate groups attached. As ATP is used for energy, a phosphate group is 
detached, and ADP is produced. Energy derived from glucose catabolism is 
used to recharge ADP into ATP. 


Glossary 


ATP 
(also, adenosine triphosphate) the cell’s energy currency 


glycolysis 
the process of breaking glucose into two three-carbon molecules with 
the production of ATP and NADH 


Biogeochemical Cycles EnBio 
By the end of this section, you will be able to: 


e Discuss the biogeochemical cycles of water, carbon, nitrogen, 
phosphorus, and sulfur 

e Explain how human activities have impacted these cycles and the 
resulting potential consequences for Earth 


Energy flows directionally through ecosystems, entering as sunlight (or 
inorganic molecules for chemoautotrophs) and leaving as heat during the 
transfers between trophic levels. Rather than flowing through an ecosystem, 
the matter that makes up living organisms is conserved and recycled. The 
six most common elements associated with organic molecules—carbon, 
nitrogen, hydrogen, oxygen, phosphorus, and sulfur—take a variety of 
chemical forms and may exist for long periods in the atmosphere, on land, 
in water, or beneath Earth’s surface. Geologic processes, such as 
weathering, erosion, water drainage, and the subduction of the continental 
plates, all play a role in the cycling of elements on Earth. Because geology 
and chemistry have major roles in the study of this process, the recycling of 
inorganic matter between living organisms and their nonliving environment 
is called a biogeochemical cycle. 


Water, which contains hydrogen and oxygen, is essential to all living 
processes. The hydrosphere is the area of Earth where water movement 
and storage occurs: as liquid water on the surface (rivers, lakes, oceans) and 
beneath the surface (groundwater) or ice, (polar ice caps and glaciers), and 
as water vapor in the atmosphere. Carbon is found in all organic 
macromolecules and is an important constituent of fossil fuels. Nitrogen is a 
major component of our nucleic acids and proteins and is critical to human 
agriculture. Phosphorus, a major component of nucleic acids, is one of the 
main ingredients (along with nitrogen) in artificial fertilizers used in 
agriculture, which has environmental impacts on our surface water. Sulfur, 
critical to the three-dimensional folding of proteins (as in disulfide binding), 
is released into the atmosphere by the burning of fossil fuels. 


The cycling of these elements is interconnected. For example, the 
movement of water is critical for the leaching of nitrogen and phosphate 
into rivers, lakes, and oceans. The ocean is also a major reservoir for 


carbon. Thus, mineral nutrients are cycled, either rapidly or slowly, through 
the entire biosphere between the biotic and abiotic world and from one 
living organism to another. 


Note: 
Concept in Action 


Head to this website to learn more about biogeochemical cycles. 


The Water Cycle 


Water is essential for all living processes. The human body is more than 
one-half water and human cells are more than 70 percent water. Thus, most 
land animals need a supply of fresh water to survive. Of the stores of water 
on Earth, 97.5 percent is salt water ([link]). Of the remaining water, 99 
percent is locked as underground water or ice. Thus, less than one percent 
of fresh water is present in lakes and rivers. Many living things are 
dependent on this small amount of surface fresh water supply, a lack of 
which can have important effects on ecosystem dynamics. Humans, of 
course, have developed technologies to increase water availability, such as 
digging wells to harvest groundwater, storing rainwater, and using 
desalination to obtain drinkable water from the ocean. Although this pursuit 
of drinkable water has been ongoing throughout human history, the supply 
of fresh water continues to be a major issue in modern times. 


Freshwater 2.5% 
(35,000,000 km?) 


Lakes and rivers 0.3% == 


Groundwater (soil moisture, swamp 
water, permafrost) 30.8% 


Glaciers and permanent snow cover 
68.9% 


Only 2.5 percent of water on Earth is fresh water, 
and less than 1 percent of fresh water is easily 
accessible to living things. 


The various processes that occur during the cycling of water are illustrated 
in [link]. The processes include the following: 


e evaporation and sublimation 

¢ condensation and precipitation 
e subsurface water flow 

e surface runoff and snowmelt 

e streamflow 


The water cycle is driven by the Sun’s energy as it warms the oceans and 
other surface waters. This leads to evaporation (water to water vapor) of 
liquid surface water and sublimation (ice to water vapor) of frozen water, 
thus moving large amounts of water into the atmosphere as water vapor. 
Over time, this water vapor condenses into clouds as liquid or frozen 
droplets and eventually leads to precipitation (rain or snow), which returns 
water to Earth’s surface. Rain reaching Earth’s surface may evaporate 
again, flow over the surface, or percolate into the ground. Most easily 
observed is surface runoff: the flow of fresh water either from rain or 
melting ice. Runoff can make its way through streams and lakes to the 
oceans or flow directly to the oceans themselves. 


Groundwater is a significant reservoir of fresh water. It exists in the pores 
between particles in sand and gravel, or in the fissures in rocks. Shallow 
groundwater flows slowly through these pores and fissures and eventually 
finds its way to a stream or lake where it becomes a part of the surface 
water again. Streams do not flow because they are replenished from 
rainwater directly; they flow because there is a constant inflow from 
groundwater below. Some groundwater is found very deep in the bedrock 
and can persist there for millennia. Most groundwater reservoirs, or 
aquifers, are the source of drinking or irrigation water drawn up through 
wells. In many cases these aquifers are being depleted faster than they are 
being replenished by water percolating down from above. 


Volcanic = —__ 
steam Y 7 — 
+ Water in the atmosphere 


Conde 


Sublimation 


Evapolrainspiration ; 
P Evaporation 


1 \e oe 
Infiltration >) 
\ \ AN 


Water from the land and oceans enters the atmosphere by 
evaporation or sublimation, where it condenses into clouds and 
falls as rain or snow. Precipitated water may enter freshwater 
bodies or infiltrate the soil. The cycle is complete when surface 
or groundwater reenters the ocean. (credit: modification of 
work by John M. Evans and Howard Perlman, USGS) 


The Carbon Cycle 


Carbon is the fourth most abundant element in living organisms. Carbon is 
present in all organic molecules, and its role in the structure of 
macromolecules is of primary importance to living organisms. Carbon 
compounds contain energy, and many of these compounds from plants and 
algae have remained stored as fossilized carbon, which humans use as fuel. 
Since the 1800s, the use of fossil fuels has accelerated. As global demand 
for Earth’s limited fossil fuel supplies has risen since the beginning of the 
Industrial Revolution, the amount of carbon dioxide in our atmosphere has 
increased as the fuels are burned. This increase in carbon dioxide has been 
associated with climate change and is a major environmental concern 
worldwide. 


The carbon cycle is most easily studied as two interconnected subcycles: 
one dealing with rapid carbon exchange among living organisms and the 
other dealing with the long-term cycling of carbon through geologic 
processes. The entire carbon cycle is shown in [link]. 


Air sea gas 
exchange 


ay y / 
~., Microbial respiration —1t— 
~ and decomposition “ 


Fossil carbon | 


Carbon dioxide gas exists in the atmosphere and is dissolved in 
water. Photosynthesis converts carbon dioxide gas to organic 
carbon, and respiration cycles the organic carbon back into 
carbon dioxide gas. Long-term storage of organic carbon 
occurs when matter from living organisms is buried deep 
underground and becomes fossilized. Volcanic activity and, 
more recently, human emissions bring this stored carbon back 
into the carbon cycle. (credit: modification of work by John M. 
Evans and Howard Perlman, USGS) 


The Biological Carbon Cycle 


Living organisms are connected in many ways, even between ecosystems. 
A good example of this connection is the exchange of carbon between 
heterotrophs and autotrophs within and between ecosystems by way of 
atmospheric carbon dioxide. Carbon dioxide is the basic building block that 


autotrophs use to build multi-carbon, high-energy compounds, such as 
glucose. The energy harnessed from the Sun is used by these organisms to 
form the covalent bonds that link carbon atoms together. These chemical 
bonds store this energy for later use in the process of respiration. Most 
terrestrial autotrophs obtain their carbon dioxide directly from the 
atmosphere, while marine autotrophs acquire it in the dissolved form 
(carbonic acid, HCO3 ). However the carbon dioxide is acquired, a 
byproduct of fixing carbon in organic compounds is oxygen. Photosynthetic 
organisms are responsible for maintaining approximately 21 percent of the 
oxygen content of the atmosphere that we observe today. 


The partners in biological carbon exchange are the heterotrophs (especially 
the primary consumers, largely herbivores). Heterotrophs acquire the high- 
energy carbon compounds from the autotrophs by consuming them and 
breaking them down by respiration to obtain cellular energy, such as ATP. 
The most efficient type of respiration, aerobic respiration, requires oxygen 
obtained from the atmosphere or dissolved in water. Thus, there is a 
constant exchange of oxygen and carbon dioxide between the autotrophs 
(which need the carbon) and the heterotrophs (which need the oxygen). 
Autotrophs also respire and consume the organic molecules they form: 
using oxygen and releasing carbon dioxide. They release more oxygen gas 
as a waste product of photosynthesis than they use for their own respiration; 
therefore, there is excess available for the respiration of other aerobic 
organisms. Gas exchange through the atmosphere and water is one way that 
the carbon cycle connects all living organisms on Earth. 


The Biogeochemical Carbon Cycle 


The movement of carbon through land, water, and air is complex, and, in 
many cases, it occurs much more slowly geologically than the movement 
between living organisms. Carbon is stored for long periods in what are 
known as carbon reservoirs, which include the atmosphere, bodies of liquid 
water (mostly oceans), ocean sediment, soil, rocks (including fossil fuels), 
and Earth’s interior. 


As stated, the atmosphere is a major reservoir of carbon in the form of 
carbon dioxide that is essential to the process of photosynthesis. The level 
of carbon dioxide in the atmosphere is greatly influenced by the reservoir of 
carbon in the oceans. The exchange of carbon between the atmosphere and 
water reservoirs influences how much carbon is found in each, and each one 
affects the other reciprocally. Carbon dioxide (CO>) from the atmosphere 
dissolves in water and, unlike oxygen and nitrogen gas, reacts with water 
molecules to form ionic compounds. Some of these ions combine with 
calcium ions in the seawater to form calcium carbonate (CaCO3), a major 
component of the shells of marine organisms. These organisms eventually 
form sediments on the ocean floor. Over geologic time, the calcium 
carbonate forms limestone, which comprises the largest carbon reservoir on 
Earth. 


On land, carbon is stored in soil as organic carbon as a result of the 
decomposition of living organisms or from weathering of terrestrial rock 
and minerals. Deeper under the ground, at land and at sea, are fossil fuels, 
the anaerobically decomposed remains of plants that take millions of years 
to form. Fossil fuels are considered a non-renewable resource because their 
use far exceeds their rate of formation. A non-renewable resource is either 
regenerated very slowly or not at all. Another way for carbon to enter the 
atmosphere is from land (including land beneath the surface of the ocean) 
by the eruption of volcanoes and other geothermal systems. Carbon 
sediments from the ocean floor are taken deep within Earth by the process 
of subduction: the movement of one tectonic plate beneath another. Carbon 
is released as carbon dioxide when a volcano erupts or from volcanic 
hydrothermal vents. 


Carbon dioxide is also added to the atmosphere by the animal husbandry 
practices of humans. The large number of land animals raised to feed 
Earth’s growing human population results in increased carbon-dioxide 
levels in the atmosphere caused by their respiration. This is another 
example of how human activity indirectly affects biogeochemical cycles in 
a significant way. Although much of the debate about the future effects of 
increasing atmospheric carbon on climate change focuses on fossils fuels, 
scientists take natural processes, such as volcanoes, plant growth, soil 


carbon levels, and respiration, into account as they model and predict the 
future impact of this increase. 


The Nitrogen Cycle 


Getting nitrogen into the living world is difficult. Plants and phytoplankton 
are not equipped to incorporate nitrogen from the atmosphere (which exists 
as tightly bonded, triple covalent Nz) even though this molecule comprises 
approximately 78 percent of the atmosphere. Nitrogen enters the living 
world via free-living and symbiotic bacteria, which incorporate nitrogen 
into their macromolecules through nitrogen fixation (conversion of N>). 
Cyanobacteria live in most aquatic ecosystems where sunlight is present; 
they play a key role in nitrogen fixation. Cyanobacteria are able to use 
inorganic sources of nitrogen to “fix” nitrogen. Rhizobium bacteria live 
symbiotically in the root nodules of legumes (such as peas, beans, and 
peanuts) and provide them with the organic nitrogen they need. Free-living 
bacteria, such as Azotobacter, are also important nitrogen fixers. Organic 
nitrogen is especially important to the study of ecosystem dynamics since 
many ecosystem processes, such as primary production and decomposition, 
are limited by the available supply of nitrogen. 


Human activity can release nitrogen into the environment by two primary 
means: the combustion of fossil fuels, which releases different nitrogen 
oxides, and by the use of artificial fertilizers (which contain nitrogen and 
phosphorus compounds) in agriculture, which are then washed into lakes, 
streams, and rivers by surface runoff. Atmospheric nitrogen (other than N>) 
is associated with several effects on Earth’s ecosystems including the 
production of acid rain (as nitric acid, HNO3) and greenhouse gas effects 
(as nitrous oxide, NO), potentially causing climate change. A major effect 
from fertilizer runoff is saltwater and freshwater eutrophication, a process 
whereby nutrient runoff causes the overgrowth of algae and a number of 
consequential problems. 


A similar process occurs in the marine nitrogen cycle, where the 
ammonification, nitrification, and denitrification processes are performed 
by marine bacteria and archaea. Some of this nitrogen falls to the ocean 
floor as sediment, which can then be moved to land in geologic time by 


uplift of Earth’s surface, and thereby incorporated into terrestrial rock. 
Although the movement of nitrogen from rock directly into living systems 
has been traditionally seen as insignificant compared with nitrogen fixed 
from the atmosphere, a recent study showed that this process may indeed be 
significant and should be included in any study of the global nitrogen cycle. 
[footnote] 

Scott L. Morford, Benjamin Z. Houlton, and Randy A. Dahlgren, 
“Increased Forest Ecosystem Carbon and Nitrogen Storage from Nitrogen 
Rich Bedrock,” Nature 477, no. 7362 (2011): 78-81. 


The Phosphorus Cycle 


Phosphorus is an essential nutrient for living processes; it is a major 
component of nucleic acids and phospholipids, and, as calcium phosphate, 
makes up the supportive components of our bones. Phosphorus is often the 
limiting nutrient (necessary for growth) in aquatic, particularly freshwater, 
ecosystems. 


Phosphorus occurs in nature as the phosphate ion (PO,*). In addition to 
phosphate runoff as a result of human activity, natural surface runoff occurs 
when it is leached from phosphate-containing rock by weathering, thus 
sending phosphates into rivers, lakes, and the ocean. This rock has its 
origins in the ocean. Phosphate-containing ocean sediments form primarily 
from the bodies of ocean organisms and from their excretions. However, 
volcanic ash, aerosols, and mineral dust may also be significant phosphate 
sources. This sediment then is moved to land over geologic time by the 
uplifting of Earth’s surface. ({link]) 


Excess phosphorus and nitrogen that enter these ecosystems from fertilizer 
runoff and from sewage cause excessive growth of algae. The subsequent 
death and decay of these organisms depletes dissolved oxygen, which leads 
to the death of aquatic organisms, such as shellfish and finfish. This process 
is responsible for dead zones in lakes and at the mouths of many major 
rivers and for massive fish kills, which often occur during the summer 
months (see [link]). 


Particulate Organic Carbon (mg/m') Population Density (persons/km’) Dead Zone Size (km’) 


unkown « . + 
10 20 $0 100 ©6200 $00 1,000 ! 10 100 1,000 10k 100k 0.1 § 10 100 Ik 10k 


Dead zones occur when phosphorus and nitrogen from 
fertilizers cause excessive growth of microorganisms, which 
depletes oxygen and kills fauna. Worldwide, large dead zones 
are found in areas of high population density. (credit: Robert 
Simmon, Jesse Allen, NASA Earth Observatory) 


A dead zone is an area in lakes and oceans near the mouths of rivers where 
large areas are periodically depleted of their normal flora and fauna; these 
zones can be caused by eutrophication, oil spills, dumping toxic chemicals, 
and other human activities. The number of dead zones has increased for 
several years, and more than 400 of these zones were present as of 2008. 
One of the worst dead zones is off the coast of the United States in the Gulf 
of Mexico: fertilizer runoff from the Mississippi River basin created a dead 
zone of over 8,463 square miles. Phosphate and nitrate runoff from 
fertilizers also negatively affect several lake and bay ecosystems including 
the Chesapeake Bay in the eastern United States. 


Note: 


Careers in Action 
Chesapeake Bay 


(a) 


This (a) satellite image shows the 
Chesapeake Bay, an ecosystem 
affected by phosphate and nitrate 
runoff. A (b) member of the Army 
Corps of Engineers holds a clump of 
oysters being used as a part of the 
oyster restoration effort in the bay. 
(credit a: modification of work by 
NASA/MODIS; credit b: modification 
of work by U.S. Army) 


The Chesapeake Bay ([link]a) is one of the most scenic areas on Earth; it is 
now in distress and is recognized as a case study of a declining ecosystem. 
In the 1970s, the Chesapeake Bay was one of the first aquatic ecosystems 
to have identified dead zones, which continue to kill many fish and 
bottom-dwelling species such as clams, oysters, and worms. Several 
species have declined in the Chesapeake Bay because surface water runoff 
contains excess nutrients from artificial fertilizer use on land. The source 
of the fertilizers (with high nitrogen and phosphate content) is not limited 


to agricultural practices. There are many nearby urban areas and more than 
150 rivers and streams empty into the bay that are carrying fertilizer runoff 
from lawns and gardens. Thus, the decline of the Chesapeake Bay is a 
complex issue and requires the cooperation of industry, agriculture, and 
individual homeowners. 

Of particular interest to conservationists is the oyster population ({link]b); 
it is estimated that more than 200,000 acres of oyster reefs existed in the 
bay in the 1700s, but that number has now declined to only 36,000 acres. 
Oyster harvesting was once a major industry for Chesapeake Bay, but it 
declined 88 percent between 1982 and 2007. This decline was caused not 
only by fertilizer runoff and dead zones, but also because of 
overharvesting. Oysters require a certain minimum population density 
because they must be in close proximity to reproduce. Human activity has 
altered the oyster population and locations, thus greatly disrupting the 
ecosystem. 

The restoration of the oyster population in the Chesapeake Bay has been 
ongoing for several years with mixed success. Not only do many people 
find oysters good to eat, but the oysters also clean up the bay. They are 
filter feeders, and as they eat, they clean the water around them. Filter 
feeders eat by pumping a continuous stream of water over finely divided 
appendages (gills in the case of oysters) and capturing prokaryotes, 
plankton, and fine organic particles in their mucus. In the 1700s, it was 
estimated that it took only a few days for the oyster population to filter the 
entire volume of the bay. Today, with the changed water conditions, it is 
estimated that the present population would take nearly a year to do the 
same job. 

Restoration efforts have been ongoing for several years by non-profit 
organizations such as the Chesapeake Bay Foundation. The restoration 
goal is to find a way to increase population density so the oysters can 
reproduce more efficiently. Many disease-resistant varieties (developed at 
the Virginia Institute of Marine Science for the College of William and 
Mary) are now available and have been used in the construction of 
experimental oyster reefs. Efforts by Virginia and Delaware to clean and 
restore the bay have been hampered because much of the pollution entering 
the bay comes from other states, which emphasizes the need for interstate 
cooperation to gain successful restoration. 


The new, hearty oyster strains have also spawned a new and economically 
viable industry—oyster aquaculture—which not only supplies oysters for 
food and profit, but also has the added benefit of cleaning the bay. 


Section Summary 


Mineral nutrients are cycled through ecosystems and their environment. Of 
particular importance are water, carbon, nitrogen, phosphorus, and sulfur. 
All of these cycles have major impacts on ecosystem structure and function. 
As human activities have caused major disturbances to these cycles, their 
study and modeling is especially important. Ecosystems have been 
damaged by a variety of human activities that alter the natural 
biogeochemical cycles due to pollution, oil spills, and events causing global 
climate change. The health of the biosphere depends on understanding these 
cycles and how to protect the environment from irreversible damage. 


Glossary 


acid rain 
a corrosive rain caused by rainwater mixing with sulfur dioxide gas as 
it fall through the atmosphere, turning it into weak sulfuric acid, 
causing damage to aquatic ecosystems 


biogeochemical cycle 
the cycling of minerals and nutrients through the biotic and abiotic 
world 


dead zone 
an area in a lake and ocean near the mouths of rivers where large areas 
are depleted of their normal flora and fauna; these zones can be caused 
by eutrophication, oil spills, dumping of toxic chemicals, and other 
human activities 


eutrophication 


the process whereby nutrient runoff causes the excess growth of 
microorganisms and plants in aquatic systems 


fallout 
the direct deposition of solid minerals on land or in the ocean from the 
atmosphere 


hydrosphere 
the region of the planet in which water exists, including the 
atmosphere that contains water vapor and the region beneath the 
ground that contains groundwater 


non-renewable resource 
a resource, such as a fossil fuel, that is either regenerated very slowly 
or not at all 


subduction 
the movement of one tectonic plate beneath another 


Biotechnology in Medicine and Agriculture EnBio 
By the end of this section, you will be able to: 


e Describe uses of biotechnology in medicine 
e Describe uses of biotechnology in agriculture 


It is easy to see how biotechnology can be used for medicinal purposes. 
Knowledge of the genetic makeup of our species, the genetic basis of 
heritable diseases, and the invention of technology to manipulate and fix 
mutant genes provides methods to treat diseases. Biotechnology in 
agriculture can enhance resistance to disease, pests, and environmental 
stress to improve both crop yield and quality. 


Genetic Diagnosis and Gene Therapy 


The process of testing for suspected genetic defects before administering 
treatment is called genetic diagnosis by genetic testing. In some cases in 
which a genetic disease is present in an individual’s family, family members 
may be advised to undergo genetic testing. For example, mutations in the 
BRCA genes may increase the likelihood of developing breast and ovarian 
cancers in women and some other cancers in women and men. A woman 
with breast cancer can be screened for these mutations. If one of the high- 
risk mutations is found, her female relatives may also wish to be screened 
for that particular mutation, or simply be more vigilant for the occurrence of 
cancers. Genetic testing is also offered for fetuses (or embryos with in vitro 
fertilization) to determine the presence or absence of disease-causing genes 
in families with specific debilitating diseases. 


Note: 
Concept in Action 


Csr . 
— 
mess Openstax COLLEGE 


See how human DNA is extracted for uses such as genetic testing. 


Gene therapy is a genetic engineering technique that may one day be used 
to cure certain genetic diseases. In its simplest form, it involves the 
introduction of a non-mutated gene at a random location in the genome to 
cure a disease by replacing a protein that may be absent in these individuals 
because of a genetic mutation. The non-mutated gene is usually introduced 
into diseased cells as part of a vector transmitted by a virus, such as an 
adenovirus, that can infect the host cell and deliver the foreign DNA into 
the genome of the targeted cell ({link]). To date, gene therapies have been 
primarily experimental procedures in humans. A few of these experimental 
treatments have been successful, but the methods may be important in the 
future as the factors limiting its success are resolved. 


Viral New Viral 
DNA Gene DNA 


Modified DNA injected 
into vecte 


Vector 
(adenovirus) 


Vector bindsto 
cell membrane 


Vector injectsnew oa 
i geneintonucleus 


13 nd ez 


Vesicle breaks 
down releasing 
vector 


Ly » 


Cell makes protein 
‘ usingnew gene 
therapy using catia 
denovirus vectors 

_ aaa 


- 


“ 


This diagram shows the steps involved in curing 
disease with gene therapy using an adenovirus 
vector. (credit: modification of work by NIH) 


Production of Hormones 


Recombinant DNA technology was used to produce large-scale quantities 
of the human hormone insulin in E. coli as early as 1978. Previously, it was 
only possible to treat diabetes with pig insulin, which caused allergic 
reactions in many humans because of differences in the insulin molecule. In 
addition, human growth hormone (HGH) is used to treat growth disorders 
in children. The HGH gene was cloned from a cDNA (complementary 
DNA) library and inserted into E. coli cells by cloning it into a bacterial 
vector. 


Transgenic Animals 


Although several recombinant proteins used in medicine are successfully 
produced in bacteria, some proteins need a eukaryotic animal host for 
proper processing. For this reason, genes have been cloned and expressed in 
animals such as sheep, goats, chickens, and mice. Animals that have been 
modified to express recombinant DNA are called transgenic animals 
((link]). 


It can be seen that two of these 
mice are transgenic because 
they have a gene that causes 

them to fluoresce under a UV 

light. The non-transgenic mouse 
does not have the gene that 
causes fluorescence. (credit: 
Ingrid Moen et al.) 


Several human proteins are expressed in the milk of transgenic sheep and 
goats. In one commercial example, the FDA has approved a blood 
anticoagulant protein that is produced in the milk of transgenic goats for use 
in humans. Mice have been used extensively for expressing and studying 
the effects of recombinant genes and mutations. 


Transgenic Plants 


Manipulating the DNA of plants (creating genetically modified organisms, 
or GMOs) has helped to create desirable traits such as disease resistance, 
herbicide, and pest resistance, better nutritional value, and better shelf life 
({link]). Plants are the most important source of food for the human 
population. Farmers developed ways to select for plant varieties with 
desirable traits long before modern-day biotechnology practices were 
established. 


Corn, a major agricultural 
crop used to create 
products for a variety of 
industries, is often 
modified through plant 
biotechnology. (credit: 
Keith Weller, USDA) 


Transgenic plants have received DNA from other species. Because they 
contain unique combinations of genes and are not restricted to the 
laboratory, transgenic plants and other GMOs are closely monitored by 
government agencies to ensure that they are fit for human consumption and 
do not endanger other plant and animal life. Because foreign genes can 
spread to other species in the environment, particularly in the pollen and 
seeds of plants, extensive testing is required to ensure ecological stability. 
Staples like corn, potatoes, and tomatoes were the first crop plants to be 
genetically engineered. 


Transformation of Plants Using Agrobacterium tumefaciens 


In plants, tumors caused by the bacterium Agrobacterium tumefaciens occur 
by transfer of DNA from the bacterium to the plant. The artificial 
introduction of DNA into plant cells is more challenging than in animal 
cells because of the thick plant cell wall. Researchers used the natural 
transfer of DNA from Agrobacterium to a plant host to introduce DNA 
fragments of their choice into plant hosts. In nature, the disease-causing A. 
tumefaciens have a set of plasmids that contain genes that integrate into the 
infected plant cell’s genome. Researchers manipulate the plasmids to carry 
the desired DNA fragment and insert it into the plant genome. 


The Organic Insecticide Bacillus thuringiensis 


Bacillus thuringiensis (Bt) is a bacterium that produces protein crystals that 
are toxic to many insect species that feed on plants. Insects that have eaten 
Bt toxin stop feeding on the plants within a few hours. After the toxin is 
activated in the intestines of the insects, death occurs within a couple of 
days. The crystal toxin genes have been cloned from the bacterium and 
introduced into plants, therefore allowing plants to produce their own 
crystal Bt toxin that acts against insects. Bt toxin is safe for the environment 
and non-toxic to mammals (including humans). As a result, it has been 
approved for use by organic farmers as a natural insecticide. There is some 


concern, however, that insects may evolve resistance to the Bt toxin in the 
same way that bacteria evolve resistance to antibiotics. 


Section Summary 


Genetic testing is performed to identify disease-causing genes, and can be 
used to benefit affected individuals and their relatives who have not 
developed disease symptoms yet. Gene therapy—by which functioning 
genes are incorporated into the genomes of individuals with a non- 
functioning mutant gene—has the potential to cure heritable diseases. 
Transgenic organisms possess DNA from a different species, usually 
generated by molecular cloning techniques. Vaccines, antibiotics, and 
hormones are examples of products obtained by recombinant DNA 
technology. Transgenic animals have been created for experimental 
purposes and some are used to produce some human proteins. 


Genes are inserted into plants, using plasmids in the bacterium 
Agrobacterium tumefaciens, which infects plants. Transgenic plants have 
been created to improve the characteristics of crop plants—for example, by 
giving them insect resistance by inserting a gene for a bacterial toxin. 


Glossary 


gene therapy 
the technique used to cure heritable diseases by replacing mutant genes 
with good genes 


genetic testing 
identifying gene variants in an individual that may lead to a genetic 
disease in that individual 


The Cell Cycle EnBio 
By the end of this section, you will be able to: 


e Describe the three stages of interphase 

e Discuss the behavior of chromosomes during mitosis and how the 
cytoplasmic content divides during cytokinesis 

e Define the quiescent Gp phase 


The cell cycle is an ordered series of events involving cell growth and cell 
division that produces two new daughter cells. Cells on the path to cell 
division proceed through a series of precisely timed and carefully regulated 
stages of growth, DNA replication, and division that produce two 
genetically identical cells. The cell cycle has two major phases: interphase 
and the mitotic phase ({link]). During interphase, the cell grows and DNA 
is replicated. During the mitotic phase, the replicated DNA and 
cytoplasmic contents are separated and the cell divides. Watch this video 
about the cell cycle: https://www. youtube.com/watch?v=Wy3N5NCZBHQ 


Mitotic Phase 


Interphase 
Mitosis Formation 
Cytokinesis of 2 daughter 


cells 


Interphase Interphase 


A cell moves through a series of phases in an orderly 
manner. During interphase, G involves cell growth and 
protein synthesis, the S phase involves DNA replication 

and the replication of the centrosome, and G> involves 


further growth and protein synthesis. The mitotic phase 
follows interphase. Mitosis is nuclear division during 
which duplicated chromosomes are segregated and 
distributed into daughter nuclei. Usually the cell will 
divide after mitosis in a process called cytokinesis in 
which the cytoplasm is divided and two daughter cells 
are formed. 


The Mitotic Phase 


To make two daughter cells, the contents of the nucleus and the cytoplasm 
must be divided. The mitotic phase is a multistep process during which the 
duplicated chromosomes are aligned, separated, and moved to opposite 
poles of the cell, and then the cell is divided into two new identical daughter 
cells. The first portion of the mitotic phase, mitosis, is composed of five 
stages, which accomplish nuclear division. The second portion of the 
mitotic phase, called cytokinesis, is the physical separation of the 
cytoplasmic components into two daughter cells. 


Section Summary 


The cell cycle is an orderly sequence of events. Cells on the path to cell 
division proceed through a series of precisely timed and carefully regulated 
stages. In eukaryotes, the cell cycle consists of a long preparatory period, 
called interphase. Interphase is divided into Gj, S, and G> phases. Mitosis 
consists of five stages: prophase, prometaphase, metaphase, anaphase, and 
telophase. Mitosis is usually accompanied by cytokinesis, during which the 
cytoplasmic components of the daughter cells are separated either by an 
actin ring (animal cells) or by cell plate formation (plant cells). 


Glossary 


anaphase 


the stage of mitosis during which sister chromatids are separated from 
each other 


cell cycle 
the ordered sequence of events that a cell passes through between one 
cell division and the next 


cell cycle checkpoints 
mechanisms that monitor the preparedness of a eukaryotic cell to 
advance through the various cell cycle stages 


cell plate 
a structure formed during plant-cell cytokinesis by Golgi vesicles 
fusing at the metaphase plate; will ultimately lead to formation of a 
cell wall to separate the two daughter cells 


centriole 
a paired rod-like structure constructed of microtubules at the center of 
each animal cell centrosome 


cleavage furrow 
a constriction formed by the actin ring during animal-cell cytokinesis 
that leads to cytoplasmic division 


cytokinesis 
the division of the cytoplasm following mitosis to form two daughter 
cells 


Go phase 
a cell-cycle phase distinct from the G, phase of interphase; a cell in Gg 
is not preparing to divide 

G, phase 
(also, first gap) a cell-cycle phase; first phase of interphase centered on 


cell growth during mitosis 


G> phase 


(also, second gap) a cell-cycle phase; third phase of interphase where 
the cell undergoes the final preparations for mitosis 


interphase 
the period of the cell cycle leading up to mitosis; includes G,, S, and 
G> phases; the interim between two consecutive cell divisions 


kinetochore 
a protein structure in the centromere of each sister chromatid that 
attracts and binds spindle microtubules during prometaphase 


metaphase plate 
the equatorial plane midway between two poles of a cell where the 
chromosomes align during metaphase 


metaphase 
the stage of mitosis during which chromosomes are lined up at the 
metaphase plate 


mitosis 
the period of the cell cycle at which the duplicated chromosomes are 
separated into identical nuclei; includes prophase, prometaphase, 
metaphase, anaphase, and telophase 


mitotic phase 
the period of the cell cycle when duplicated chromosomes are 
distributed into two nuclei and the cytoplasmic contents are divided; 
includes mitosis and cytokinesis 


mitotic spindle 
the microtubule apparatus that orchestrates the movement of 
chromosomes during mitosis 


prometaphase 
the stage of mitosis during which mitotic spindle fibers attach to 
kinetochores 


prophase 


the stage of mitosis during which chromosomes condense and the 
mitotic spindle begins to form 


quiescent 
describes a cell that is performing normal cell functions and has not 
initiated preparations for cell division 


S phase 
the second, or synthesis phase, of interphase during which DNA 
replication occurs 


telophase 
the stage of mitosis during which chromosomes arrive at opposite 
poles, decondense, and are surrounded by new nuclear envelopes 


Cloning and Genetic Engineering EnBio 
By the end of this section, you will be able to: 


e Explain the basic techniques used to manipulate genetic material 
e Explain molecular and reproductive cloning 


Biotechnology is the use of artificial methods to modify the genetic 
material of living organisms or cells to produce novel compounds or to 
perform new functions. Biotechnology has been used for improving 
livestock and crops since the beginning of agriculture through selective 
breeding. Since the discovery of the structure of DNA in 1953, and 
particularly since the development of tools and methods to manipulate 
DNA in the 1970s, biotechnology has become synonymous with the 
manipulation of organisms’ DNA at the molecular level. The primary 
applications of this technology are in medicine (for the production of 
vaccines and antibiotics) and in agriculture (for the genetic modification of 
crops). 


Manipulating Genetic Material 


To accomplish the applications described above, biotechnologists must be 
able to extract, manipulate, and analyze nucleic acids. 


Review of Nucleic Acid Structure 


To understand the basic techniques used to work with nucleic acids, 
remember that nucleic acids are macromolecules made of nucleotides (a 
sugar, a phosphate, and a nitrogenous base). The phosphate groups on these 
molecules each have a net negative charge. An entire set of DNA molecules 
in the nucleus of eukaryotic organisms is called the genome. DNA has two 
complementary strands linked by hydrogen bonds between the paired bases. 


Unlike DNA in eukaryotic cells, RNA molecules leave the nucleus. 
Messenger RNA (mRNA) is analyzed most frequently because it represents 
the protein-coding genes that are being expressed in the cell. 


Isolation of Nucleic Acids 


To study or manipulate nucleic acids, the DNA must first be extracted from 
cells. Various techniques are used to extract different types of DNA ((link]). 
Most nucleic acid extraction techniques involve steps to break open the cell, 
and then the use of enzymatic reactions to destroy all undesired 
macromolecules. Cells are broken open using a detergent solution 
containing buffering compounds. To prevent degradation and 
contamination, macromolecules such as proteins and RNA are inactivated 
using enzymes. The DNA is then brought out of solution using alcohol. The 
resulting DNA, because it is made up of long polymers, forms a gelatinous 
mass. 


DNA Extraction 


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Cells are lysed Cell contents Cell debris is The DNA is 


using a detergent are treated with pelleted ina precipitated 
that disrupts the protease to centrifuge. The with ethanol. 
plasma membrane. destroy protein supernatant (liquid) It forms viscous 
and RNase to containing the DNA strands that can 
destroy RNA. is transferred toa be spooled on 
clean tube. a glass rod. 


This diagram shows the basic method used for the 
extraction of DNA. 


RNA is studied to understand gene expression patterns in cells. RNA is 
naturally very unstable because enzymes that break down RNA are 
commonly present in nature. Some are even secreted by our own skin and 
are very difficult to inactivate. Similar to DNA extraction, RNA extraction 


involves the use of various buffers and enzymes to inactivate other 
macromolecules and preserve only the RNA. 


Gel Electrophoresis 


Because nucleic acids are negatively charged ions at neutral or alkaline pH 
in an aqueous environment, they can be moved by an electric field. Gel 
electrophoresis is a technique used to separate charged molecules on the 
basis of size and charge. The nucleic acids can be separated as whole 
chromosomes or as fragments. The nucleic acids are loaded into a slot at 
one end of a gel matrix, an electric current is applied, and negatively 
charged molecules are pulled toward the opposite end of the gel (the end 
with the positive electrode). Smaller molecules move through the pores in 
the gel faster than larger molecules; this difference in the rate of migration 
separates the fragments on the basis of size. The nucleic acids in a gel 
matrix are invisible until they are stained with a compound that allows them 
to be seen, such as a dye. Distinct fragments of nucleic acids appear as 
bands at specific distances from the top of the gel (the negative electrode 
end) that are based on their size ((link]). A mixture of many fragments of 
varying sizes appear as a long smear, whereas uncut genomic DNA is 
usually too large to run through the gel and forms a single large band at the 
top of the gel. 


Larger fragments 


Smaller fragments 


Shown are DNA fragments from six samples 
run on a gel, stained with a fluorescent dye 
and viewed under UV light. (credit: 
modification of work by James Jacob, 
Tompkins Cortland Community College) 


Polymerase Chain Reaction 


DNA analysis often requires focusing on one or more specific regions of 
the genome. It also frequently involves situations in which only one or a 
few copies of a DNA molecule are available for further analysis. These 
amounts are insufficient for most procedures, such as gel electrophoresis. 
Polymerase chain reaction (PCR) is a technique used to rapidly increase 
the number of copies of specific regions of DNA for further analyses 
({link]). PCR uses a special form of DNA polymerase, the enzyme that 


replicates DNA, and other short nucleotide sequences called primers that 
base pair to a specific portion of the DNA being replicated. PCR is used for 
many purposes in laboratories. These include: 1) the identification of the 
owner of a DNA sample left at a crime scene; 2) paternity analysis; 3) the 
comparison of small amounts of ancient DNA with modern organisms; and 
4) determining the sequence of nucleotides in a specific region. 


Double-stranded DNA 


3 5’ 
Cet =. 


Denaturation 
at 95°C 


Annealing Primer 1 


at ~50°C Primer 2 


1 


Extension DNA polymerase 
at 72°C 


| 


QUUUUTUATUEUTOATOEAT CATA TCE TET TT 
Increase PUY UAT OETTETTETTETT CATE TET TET PE 


copies 
TOUTE OATETE OETA EEE ET EEE ETT 
QUUUCU TET OETET TATE TA TEA TATE TET PA 


Polymerase chain reaction, or 
PCR, is used to produce many 
copies of a specific sequence of 


DNA using a special form of DNA 
polymerase. 


Cloning 


In general, cloning means the creation of a perfect replica. Typically, the 
word is used to describe the creation of a genetically identical copy. In 
biology, the re-creation of a whole organism is referred to as “reproductive 
cloning.” Long before attempts were made to clone an entire organism, 
researchers learned how to copy short stretches of DNA—a process that is 
referred to as molecular cloning. 


Molecular Cloning 


Cloning allows for the creation of multiple copies of genes, expression of 
genes, and study of specific genes. To get the DNA fragment into a 
bacterial cell in a form that will be copied or expressed, the fragment is first 
inserted into a plasmid. A plasmid (also called a vector in this context) is a 
small circular DNA molecule that replicates independently of the 
chromosomal DNA in bacteria. In cloning, the plasmid molecules can be 
used to provide a "vehicle" in which to insert a desired DNA fragment. 
Modified plasmids are usually reintroduced into a bacterial host for 
replication. As the bacteria divide, they copy their own DNA (including the 
plasmids). The inserted DNA fragment is copied along with the rest of the 
bacterial DNA. 


Plasmids occur naturally in bacterial populations (such as Escherichia coli) 
and have genes that can contribute favorable traits to the organism, such as 
antibiotic resistance (the ability to be unaffected by antibiotics). Plasmids 
have been highly engineered as vectors for molecular cloning and for the 
subsequent large-scale production of important molecules, such as insulin. 
A valuable characteristic of plasmid vectors is the ease with which a foreign 
DNA fragment can be introduced. 


Sticky ends 


(c) 


In this (a) six-nucleotide restriction enzyme recognition site, 
notice that the sequence of six nucleotides reads the same in 
the 5' to 3' direction on one strand as it does in the 5' to 3' 
direction on the complementary strand. This is known as a 
palindrome. (b) The restriction enzyme makes breaks in the 
DNA strands, and (c) the cut in the DNA results in “sticky 
ends”. Another piece of DNA cut on either end by the same 
restriction enzyme could attach to these sticky ends and be 
inserted into the gap made by this cut. 


Foreign DNA Plasmid Restriction site 

Both foreign DNA and a plasmid are 
cut with the same restriction enzyme. 
The restriction site occurs only once 
in the plasmid in the middle of a gene 
for an enzyme (lacZ). 


lacZ gene 


Ampicillin 
resistance 
gene 


The restriction enzyme leaves 
complementary sticky ends on the 
foreign DNA fragment and the 
plasmid. This allows the foreign 
DNA to be inserted into the plasmid 
when the sticky ends anneal. Adding 
DNA ligase reattaches the DNA 
backbones. These are recombinant 
plasmids. 


The plasmids are combined with a 
culture of living bacteria. Many of 

P the bacteria do not take any 
Bacteria may take up plasmids into their cells, many take 
plasmid with or without plasmids that do not have the 

the insert, or may not foreign DNA in them, and a few 
take up plasmid at all. take up the recombinant plasmid. 


The bacteria that take up the 
recombinant plasmid cannot make 
the enzyme from the gene that the 
fragment was inserted into (lacZ). 
They also carry a gene for 
resistance to the antibiotic ampicillin, 
which was on the original plasmid. 


Bacterial genome is 
missing the lacZ gene. 


White colonies To find the bacteria with the recombinant 
have plasmids plasmid, the bacteria are grown on a plate 
with the foreign with the antibiotic ampicillin and a substance 
insert. that changes color when exposed to the 
Blue colonies enzyme produced by the /acZ gene. The 
have plasmids ampicillin will kill any bacteria that did not 
without insert. take up a plasmid. The color of the substance 
will not change when the gene for /acZ 
contains the foreign DNA insert. These are 
the bacteria with the recombinant plasmid 
that we want to grow. 


This diagram shows the steps involved in molecular cloning. 


Plasmids with foreign DNA inserted into them are called recombinant 
DNA molecules because they contain new combinations of genetic 
material. Proteins that are produced from recombinant DNA molecules are 
called recombinant proteins. Not all recombinant plasmids are capable of 
expressing genes. Plasmids may also be engineered to express proteins only 
when stimulated by certain environmental factors, so that scientists can 
control the expression of the recombinant proteins. 


Reproductive Cloning 


Reproductive cloning is a method used to make a clone or an identical 
copy of an entire multicellular organism. 


Natural sexual reproduction involves the union, during fertilization, of a 
sperm and an egg. Each of these gametes is haploid, meaning they contain 
one set of chromosomes in their nuclei. The resulting cell, or zygote, is then 
diploid and contains two sets of chromosomes. This cell divides mitotically 
to produce a multicellular organism. However, the union of just any two 
cells cannot produce a viable zygote; there are components in the cytoplasm 
of the egg cell that are essential for the early development of the embryo 
during its first few cell divisions. Without these provisions, there would be 
no subsequent development. Therefore, to produce a new individual, both a 
diploid genetic complement and an egg cytoplasm are required. The 
approach to producing an artificially cloned individual is to take the egg 
cell of one individual and to remove the haploid nucleus. Then a diploid 
nucleus from a body cell of a second individual, the donor, is put into the 
egg cell. The egg is then stimulated to divide so that development proceeds. 
This sounds simple, but in fact it takes many attempts before each of the 
steps is completed successfully. 


The first cloned agricultural animal was Dolly, a sheep who was born in 
1996. The success rate of reproductive cloning at the time was very low. 
Dolly lived for six years and died of a lung tumor ([link]). There was 
speculation that because the cell DNA that gave rise to Dolly came from an 
older individual, the age of the DNA may have affected her life expectancy. 


Since Dolly, several species of animals (such as horses, bulls, and goats) 
have been successfully cloned. 


Note: 
Art Connection 
Scottish Blackface Finn-Dorset 
(Cytoplasmic Donor) (Nuclear Donor) 
Enucleation 


2 Direct current pulse 
Blastocyst ) 
SERS ie 


Surrogate 
ewe 


Dolly 


Dolly the sheep was the first 
agricultural animal to be 
cloned. To create Dolly, the 
nucleus was removed from a 
donor egg cell. The 
enucleated egg was placed 
next to the other cell, then 
they were shocked to fuse. 
They were shocked again to 
start division. The cells 
were allowed to divide for 
several days until an early 
embryonic stage was 


reached, before being 
implanted in a surrogate 
mother. 


Genetic Engineering 


Using recombinant DNA technology to modify an organism’s DNA to 
achieve desirable traits is called genetic engineering. Addition of foreign 
DNA in the form of recombinant DNA vectors that are generated by 
molecular cloning is the most common method of genetic engineering. An 
organism that receives the recombinant DNA is called a genetically 
modified organism (GMO). If the foreign DNA that is introduced comes 
from a different species, the host organism is called transgenic. Bacteria, 
plants, and animals have been genetically modified since the early 1970s 
for academic, medical, agricultural, and industrial purposes. These 
applications will be examined in more detail in the next module. 


Note: 
Concept in Action 


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mss’ OPENStax COLLEGE 


Watch this short video explaining how scientists create a transgenic animal. 


Section Summary 


Nucleic acids can be isolated from cells for the purposes of further analysis 
by breaking open the cells and enzymatically destroying all other major 
macromolecules. Fragmented or whole chromosomes can be separated on 
the basis of size by gel electrophoresis. Short stretches of DNA can be 
amplified by PCR. DNA can be cut (and subsequently re-spliced together) 
using restriction enzymes. The molecular and cellular techniques of 
biotechnology allow researchers to genetically engineer organisms, 
modifying them to achieve desirable traits. 


Cloning may involve cloning small DNA fragments (molecular cloning), or 
cloning entire organisms (reproductive cloning). In molecular cloning with 
bacteria, a desired DNA fragment is inserted into a bacterial plasmid using 
restriction enzymes and the plasmid is taken up by a bacterium, which will 
then express the foreign DNA. Using other techniques, foreign genes can be 
inserted into eukaryotic organisms. In each case, the organisms are called 
transgenic organisms. In reproductive cloning, a donor nucleus is put into 
an enucleated egg cell, which is then stimulated to divide and develop into 
an organism. 


Glossary 


anneal 
in molecular biology, the process by which two single strands of DNA 
hydrogen bond at complementary nucleotides to form a double- 
stranded molecule 


biotechnology 
the use of artificial methods to modify the genetic material of living 
organisms or cells to produce novel compounds or to perform new 
functions 


cloning 
the production of an exact copy—specifically, an exact genetic copy— 


of a gene, cell, or organism 


gel electrophoresis 


a technique used to separate molecules on the basis of their ability to 
migrate through a semisolid gel in response to an electric current 


genetic engineering 
alteration of the genetic makeup of an organism using the molecular 
methods of biotechnology 


genetically modified organism (GMO) 
an organism whose genome has been artificially changed 


plasmid 
a small circular molecule of DNA found in bacteria that replicates 
independently of the main bacterial chromosome; plasmids code for 
some important traits for bacteria and can be used as vectors to 
transport DNA into bacteria in genetic engineering applications 


polymerase chain reaction (PCR) 
a technique used to make multiple copies of DNA 


recombinant DNA 
a combination of DNA fragments generated by molecular cloning that 
does not exist in nature 


recombinant protein 
a protein that is expressed from recombinant DNA molecules 


restriction enzyme 
an enzyme that recognizes a specific nucleotide sequence in DNA and 
cuts the DNA double strand at that recognition site, often with a 
staggered cut leaving short single strands or “sticky” ends 


reverse genetics 
a form of genetic analysis that manipulates DNA to disrupt or affect 
the product of a gene to analyze the gene’s function 


reproductive cloning 
cloning of entire organisms 


transgenic 
describing an organism that receives DNA from a different species 


Community Ecology EnBio 
By the end of this section, you will be able to: 


e Discuss the predator-prey cycle 

¢ Give examples of defenses against predation and herbivory 
e Describe the competitive exclusion principle 

e Give examples of symbiotic relationships between species 
e Describe community structure and succession 


In general, populations of one species never live in isolation from 
populations of other species. The interacting populations occupying a given 
habitat form an ecological community. The number of species occupying 
the same habitat and their relative abundance is known as the diversity of 
the community. Scientists study ecology at the community level to 
understand how species interact with each other and compete for the same 
resources. 


Predation and Herbivory 


Perhaps the classical example of species interaction is the predator-prey 
relationship. The narrowest definition of the predator-prey interaction 
describes individuals of one population that kill and then consume the 
individuals of another population. Population sizes of predators and prey in 
a community are not constant over time, and they may vary in cycles that 
appear to be related. The most often cited example of predator-prey 
population dynamics is seen in the cycling of the lynx (predator) and the 
snowshoe hare (prey), using 100 years of trapping data from North America 
({link]). This cycling of predator and prey population sizes has a period of 
approximately ten years, with the predator population lagging one to two 
years behind the prey population. An apparent explanation for this pattern is 
that as the hare numbers increase, there is more food available for the lynx, 
allowing the lynx population to increase as well. When the lynx population 
grows to a threshold level, however, they kill so many hares that hare 
numbers begin to decline, followed by a decline in the lynx population 
because of scarcity of food. When the lynx population is low, the hare 
population size begins to increase due, in part, to low predation pressure, 
starting the cycle anew. 


Predator-prey Dynamics 


[Bh Hare (red) 
|_| Lynx (blue) 


Thousands of animals 


1845 1865 1885 1905 1925 
Time (years) 


The cycling of snowshoe hare and lynx 
populations in Northern Ontario is an example 
of predator-prey dynamics. 


Defense Mechanisms against Predation and Herbivory 


Predation and predator avoidance are strong selective agents. Any heritable 
character that allows an individual of a prey population to better evade its 
predators will be represented in greater numbers in later generations. 
Likewise, traits that allow a predator to more efficiently locate and capture 
its prey will lead to a greater number of offspring and an increase in the 
commonness of the trait within the population. Such ecological 
relationships between specific populations lead to adaptations that are 
driven by reciprocal evolutionary responses in those populations, a process 
called coevolution. Species have evolved numerous mechanisms to escape 
predation and herbivory (the consumption of plants for food). Defenses may 
be mechanical, chemical, physical, or behavioral. 


Mechanical defenses, such as the presence of armor in animals or thorns in 
plants, discourage predation and herbivory by discouraging physical contact 
({link]a). Many animals produce or obtain chemical defenses from plants 
and store them to prevent predation. Many plant species produce secondary 
plant compounds that serve no function for the plant except that they are 


toxic to animals and discourage consumption. For example, the foxglove 
produces several compounds, including digitalis, that are extremely toxic 
when eaten ((link]b). (Biomedical scientists have purposed the chemical 
produced by foxglove as a heart medication, which has saved lives for 
many decades.) 


The (a) honey locust tree uses thorns, a mechanical 
defense, against herbivores, while the (b) foxglove 
uses a chemical defense: toxins produces by the plant 
can cause nausea, vomiting, hallucinations, 
convulsions, or death when consumed. (credit a: 
modification of work by Huw Williams; credit b: 
modification of work by Philip Jagenstedt) 


Many species use their body shape and coloration to avoid being detected 
by predators. The tropical walking stick is an insect with the coloration and 
body shape of a twig, which makes it very hard to see when it is stationary 
against a background of real twigs ([link]a). In another example, the 
chameleon can change its color to match its surroundings ((link]b). 


(a) (b) 


(a) The tropical walking stick and (b) the chameleon use 
their body shape and/or coloration to prevent detection by 
predators. (credit a: modification of work by Linda Tanner; 
credit b: modification of work by Frank Vassen) 


Some species use coloration as a way of warning predators that they are 
distasteful or poisonous. For example, the monarch butterfly caterpillar 
sequesters poisons from its food (plants and milkweeds) to make itself 
poisonous or distasteful to potential predators. The caterpillar is bright 
yellow and black to advertise its toxicity. The caterpillar is also able to pass 
the sequestered toxins on to the adult monarch, which is also dramatically 
colored black and red as a warning to potential predators. Fire-bellied toads 
produce toxins that make them distasteful to their potential predators. They 
have bright red or orange coloration on their bellies, which they display to a 
potential predator to advertise their poisonous nature and discourage an 
attack. These are only two examples of warning coloration, which is a 
relatively common adaptation. Warning coloration only works if a predator 
uses eyesight to locate prey and can learn—a naive predator must 
experience the negative consequences of eating one before it will avoid 
other similarly colored individuals ({link]). 


The fire-bellied toad has bright 
coloration on its belly that 
serves to warn potential 
predators that it is toxic. (credit: 
modification of work by 
Roberto Verzo) 


While some predators learn to avoid eating certain potential prey because of 
their coloration, other species have evolved mechanisms to mimic this 
coloration to avoid being eaten, even though they themselves may not be 
unpleasant to eat or contain toxic chemicals. In some cases of mimicry, a 
harmless species imitates the warning coloration of a harmful species. 
Assuming they share the same predators, this coloration then protects the 
harmless ones. Many insect species mimic the coloration of wasps, which 
are stinging, venomous insects, thereby discouraging predation ((link]). 


(a) 


One form of mimicry is when a harmless species mimics 
the coloration of a harmful species, as is seen with the 
(a) wasp (Polistes sp.) and the (b) hoverfly (Syrphus 
sp.). (credit: modification of work by Tom Ings) 


In other cases of mimicry, multiple species share the same warning 
coloration, but all of them actually have defenses. The commonness of the 
signal improves the compliance of all the potential predators. [link] shows a 
variety of foul-tasting butterflies with similar coloration. 


Several unpleasant-tasting 
Heliconius butterfly species 
share a similar color pattern 

with better-tasting varieties, an 
example of mimicry. (credit: 
Joron M, Papa R, Beltran M, 
Chamberlain N, Mavarez J, et 
al.) 


Note: 
Concept in Action 


el 
Seabee 


— 
mess" Openstax COLLEGE 
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7 
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Go to this website to view stunning examples of mimicry. 


Competitive Exclusion Principle 


Resources are often limited within a habitat and multiple species may 
compete to obtain them. Ecologists have come to understand that all species 
have an ecological niche. A niche is the unique set of resources used by a 
species, which includes its interactions with other species. The competitive 
exclusion principle states that two species cannot occupy the same niche in 
a habitat: in other words, different species cannot coexist in a community if 
they are competing for all the same resources. This principle works because 
if there is an overlap in resource use and therefore competition between two 
species, then traits that lessen reliance on the shared resource will be 
selected for leading to evolution that reduces the overlap. If either species is 
unable to evolve to reduce competition, then the species that most 
efficiently exploits the resource will drive the other species to extinction. 
An experimental example of this principle is shown in [link] with two 
protozoan species: Paramecium aurelia and Paramecium caudatum. When 
grown individually in the laboratory, they both thrive. But when they are 
placed together in the same test tube (habitat), P. aurelia outcompetes P. 
caudatum for food, leading to the latter’s eventual extinction. 


P. aurelia alone P. caudatum alone Both species grown together 
250 


2 
82 
2 
ae 
o 
2 
El 
s 
Zz 


10 5 10 10 
Time (days) Time (days) Time (days) 


Paramecium aurelia and Paramecium caudatum grow well 
individually, but when they compete for the same resources, 
the P. aurelia outcompetes the P. caudatum. 


Symbiosis 


Symbiotic relationships are close, long-term interactions between 
individuals of different species. Symbioses may be commensal, in which 
one species benefits while the other is neither harmed nor benefited; 
mutualistic, in which both species benefit; or parasitic, in which the 
interaction harms one species and benefits the other. 


Commensalism 


A commensal relationship occurs when one species benefits from a close 
prolonged interaction, while the other neither benefits nor is harmed. Birds 
nesting in trees provide an example of a commensal relationship ((Link]). 
The tree is not harmed by the presence of the nest among its branches. The 
nests are light and produce little strain on the structural integrity of the 
branch, and most of the leaves, which the tree uses to get energy by 
photosynthesis, are above the nest so they are unaffected. The bird, on the 
other hand, benefits greatly. If the bird had to nest in the open, its eggs and 
young would be vulnerable to predators. Many potential commensal 
relationships are difficult to identify because it is difficult to prove that one 
partner does not derive some benefit from the presence of the other. 


The southern masked-weaver 
is Starting to make a nest ina 
tree in Zambezi Valley, 
Zambia. This is an example 
of a commensal relationship, 
in which one species (the 
bird) benefits, while the other 
(the tree) neither benefits nor 
is harmed. (credit: 
“Hanay”/Wikimedia 
Commons) 


Mutualism 


A second type of symbiotic relationship is called mutualism, in which two 
species benefit from their interaction. For example, termites have a 
mutualistic relationship with protists that live in the insect’s gut ([link]a). 
The termite benefits from the ability of the protists to digest cellulose. 
However, the protists are able to digest cellulose only because of the 
presence of symbiotic bacteria within their cells that produce the cellulase 
enzyme. The termite itself cannot do this: without the protozoa, it would not 
be able to obtain energy from its food (cellulose from the wood it chews 
and eats). The protozoa benefit by having a protective environment and a 
constant supply of food from the wood chewing actions of the termite. In 
turn, the protists benefit from the enzymes provided by their bacterial 
endosymbionts, while the bacteria benefit from a doubly protective 
environment and a constant source of nutrients from two hosts. Lichen are a 
mutualistic relationship between a fungus and photosynthetic algae or 
cyanobacteria ([link]b). The glucose produced by the algae provides 
nourishment for both organisms, whereas the physical structure of the 
lichen protects the algae from the elements and makes certain nutrients in 
the atmosphere more available to the algae. The algae of lichens can live 


independently given the right environment, but many of the fungal partners 
are unable to live on their own. 


(a) Termites form a mutualistic relationship with symbiotic 
protozoa in their guts, which allow both organisms to obtain 
energy from the cellulose the termite consumes. (b) Lichen is a 
fungus that has symbiotic photosynthetic algae living in close 
association. (credit a: modification of work by Scott Bauer, 
USDA; credit b: modification of work by Cory Zanker) 


Parasitism 


A parasite is an organism that feeds off another without immediately 
killing the organism it is feeding on. In this relationship, the parasite 
benefits, but the organism being fed upon, the host, is harmed. The host is 
usually weakened by the parasite as it siphons resources the host would 
normally use to maintain itself. Parasites may kill their hosts, but there is 
usually selection to slow down this process to allow the parasite time to 
complete its reproductive cycle before it or its offspring are able to spread 
to another host. 


The reproductive cycles of parasites are often very complex, sometimes 
requiring more than one host species. A tapeworm causes disease in 
humans when contaminated, undercooked meat such as pork, fish, or beef is 
consumed ([link]). The tapeworm can live inside the intestine of the host for 
several years, benefiting from the host’s food, and it may grow to be over 
50 feet long by adding segments. The parasite moves from one host species 
to a second host species in order to complete its life cycle. Plasmodium 
falciparum is another parasite: the protists that cause malaria, a significant 
disease in many parts of the world. Living inside human liver and red blood 
cells, the organism reproduces asexually in the human host and then 
sexually in the gut of blood-feeding mosquitoes to complete its life cycle. 
Thus malaria is spread from human to mosquito and back to human, one of 
many arthropod-borne infectious diseases of humans. 


Tapeworm (Taenia) Infection 


Embryos develop into 
larvae in muscles of Cysts may develop 
© Tapeworm embryos pigs or humans. in any organ, and are most 
hatch, penetrate the common in subcutaneous 


intestinal wall, and f tissue as well as in the 
circulate to brain and eyes. 
musculature in pigs — 
or humans. Humans acquire the 

infection by ingesting @} 

raw or undercooked 

meat from an infected 

animal host. 


a al bd 
a) The tapeworm 


2) Eggs or segments attaches itself 
are ingested by pigs to the intestine 
or humans. via hooks on 

the scolex. 


Eggs or tapeworm segments 
in feces are passed into the 
environment. 


Adults in small intestine 


This diagram shows the life cycle of the tapeworm, a 
human worm parasite. (credit: modification of work by 
CDC) 


Note: 
Concept in Action 


To learn more about “Symbiosis in the Sea,” watch this webisode of 
Jonathan Bird’s Blue World. 


Characteristics of Communities 


Communities are complex systems that can be characterized by their 
structure (the number and size of populations and their interactions) and 
dynamics (how the members and their interactions change over time). 
Understanding community structure and dynamics allows us to minimize 
impacts on ecosystems and manage ecological communities we benefit 
from. 


Biodiversity 


Ecologists have extensively studied one of the fundamental characteristics 
of communities: biodiversity. One measure of biodiversity used by 
ecologists is the number of different species in a particular area and their 
relative abundance. The area in question could be a habitat, a biome, or the 
entire biosphere. Species richness is the term used to describe the number 
of species living in a habitat or other unit. Species richness varies across the 
globe ([link]). Ecologists have struggled to understand the determinants of 
biodiversity. Species richness is related to latitude: the greatest species 
richness occurs near the equator and the lowest richness occurs near the 
poles. Other factors influence species richness as well. Island 
biogeography attempts to explain the great species richness found in 


isolated islands, and has found relationships between species richness, 
island size, and distance from the mainland. 


Relative species abundance is the number of individuals in a species 
relative to the total number of individuals in all species within a system. In 
measuring diversity the number of relatively common species is used. 
Foundation species, described below, often have the highest relative 
abundance of species. 


Number of mammal 
species per sq km 


Clo HS 94-128 

() 1-23 GM 129-154 
(5) 24-42 155-178 
@ 43-60 HM 179-228 
GS 61-93 


The greatest species richness for 
mammals in North America is 
associated in the equatorial latitudes. 
(credit: modification of work by 
NASA, CIESIN, Columbia 
University) 


Foundation Species 


Foundation species are considered the “base” or “bedrock” of a 
community, having the greatest influence on its overall structure. They are 
often primary producers, and they are typically an abundant organism. For 
example, kelp, a species of brown algae, is a foundation species that forms 
the basis of the kelp forests off the coast of California. 


Foundation species may physically modify the environment to produce and 
maintain habitats that benefit the other organisms that use them. Examples 
include the kelp described above or tree species found in a forest. The 
photosynthetic corals of the coral reef also provide structure by physically 
modifying the environment ({link]). The exoskeletons of living and dead 
coral make up most of the reef structure, which protects many other species 
from waves and ocean currents. 


Coral is the foundation species of 
coral reef ecosystems. (credit: Jim 
E. Maragos, USFWS) 


Keystone Species 


A keystone species is one whose presence has inordinate influence in 
maintaining the prevalence of various species in an ecosystem, the 
ecological community’s structure, and sometimes its biodiversity. Pisaster 
ochraceus, the intertidal sea star, is a keystone species in the northwestern 
portion of the United States ((link]). Studies have shown that when this 
organism is removed from communities, mussel populations (their natural 
prey) increase, which completely alters the species composition and reduces 
biodiversity. Another keystone species is the banded tetra, a fish in tropical 
streams, which supplies nearly all of the phosphorus, a necessary inorganic 
nutrient, to the rest of the community. The banded tetra feeds largely on 
insects from the terrestrial ecosystem and then excretes phosphorus into the 
aquatic ecosystem. The relationships between populations in the 
community, and possibly the biodiversity, would change dramatically if 
these fish were to become extinct. 


The Pisaster ochraceus sea star is 
a keystone species. (credit: Jerry 
Kirkhart) 


Community Dynamics 


Community dynamics are the changes in community structure and 
composition over time, often following environmental disturbances such 


as volcanoes, earthquakes, storms, fires, and climate change. Communities 
with a relatively constant number of species are said to be at equilibrium. 
The equilibrium is dynamic with species identities and relationships 
changing over time, but maintaining relatively constant numbers. Following 
a disturbance, the community may or may not return to the equilibrium 
state. 


Succession describes the sequential appearance and disappearance of 
species in a community over time after a severe disturbance. In primary 
succession, newly exposed or newly formed rock is colonized by living 
organisms; in secondary succession, a part of an ecosystem is disturbed 
and remnants of the previous community remain. In both cases, there is a 
sequential change in species until a more or less permanent community 
develops. 


Primary Succession and Pioneer Species 


Primary succession occurs when new land is formed, for example, 
following the eruption of volcanoes, such as those on the Big Island of 
Hawaii. As lava flows into the ocean, new land is continually being formed. 
On the Big Island, approximately 32 acres of land is added to it its size each 
year. Weathering and other natural forces break down the rock enough for 
the establishment of hearty species such as lichens and some plants, known 
as pioneer species (({link]). These species help to further break down the 
mineral-rich lava into soil where other, less hardy but more competitive 
species, such as grasses, shrubs, and trees, will grow and eventually replace 
the pioneer species. Over time the area will reach an equilibrium state, with 
a set of organisms quite different from the pioneer species. 


During primary succession in lava 
on Maui, Hawaii, succulent plants 
are the pioneer species. (credit: 
Forest and Kim Starr) 


Secondary succession 


A classic example of secondary succession occurs in oak and hickory 
forests cleared by wildfire ({link]). Wildfires will burn most vegetation, and 
unless the animals can flee the area, they are killed. Their nutrients, 
however, are returned to the ground in the form of ash. Thus, although the 
community has been dramatically altered, there is a soil ecosystem present 
that provides a foundation for rapid recolonization. 


Before the fire, the vegetation was dominated by tall trees with access to the 
major plant energy resource: sunlight. Their height gave them access to 
sunlight while also shading the ground and other low-lying species. After 
the fire, though, these trees are no longer dominant. Thus, the first plants to 
grow back are usually annual plants followed within a few years by quickly 
growing and spreading grasses and other pioneer species. Due, at least in 
part, to changes in the environment brought on by the growth of grasses and 
forbs, over many years, shrubs emerge along with small pine, oak, and 


hickory trees. These organisms are called intermediate species. Eventually, 
over 150 years, the forest will reach its equilibrium point and resemble the 
community before the fire. This equilibrium state is referred to as the 
climax community, which will remain until the next disturbance. The 
climax community is typically characteristic of a given climate and 
geology. Although the community in equilibrium looks the same once it is 
attained, the equilibrium is a dynamic one with constant changes in 
abundance and sometimes species identities. The return of a natural 
ecosystem after agricultural activities is also a well-documented secondary 
succession process. 


Secondary Succession of an Oak and Hickory Forest 


Pioneer species Intermediate species Climax community 
Annual plants grow and are succeeded Shrubs, then pines, and young oak The mature oak and hickory forest 
by grasses and perennials. and hickory begin to grow. remains stable until the next disturbance. 


Secondary succession is seen in an oak and hickory forest after a 
forest fire. A sequence of the community present at three 
successive times at the same location is depicted. 


Section Summary 


Communities include all the different species living in a given area. The 
variety of these species is referred to as biodiversity. Many organisms have 
developed defenses against predation and herbivory, including mechanical 
defenses, warning coloration, and mimicry. Two species cannot exist 
indefinitely in the same habitat competing directly for the same resources. 
Species may form symbiotic relationships such as commensalism, 


mutualism, or parasitism. Community structure is described by its 
foundation and keystone species. Communities respond to environmental 
disturbances by succession: the predictable appearance of different types of 
plant species, until a stable community structure is established. 


Glossary 


climax community 
the final stage of succession, where a stable community is formed by a 
characteristic assortment of plant and animal species 


competitive exclusion principle 
no two species within a habitat can coexist indefinitely when they 
compete for the same resources at the same time and place 


environmental disturbance 
a change in the environment caused by natural disasters or human 
activities 


foundation species 
a species which often forms the major structural portion of the habitat 


host 
an organism a parasite lives on 


island biogeography 
the study of life on island chains and how their geography interacts 
with the diversity of species found there 


keystone species 
a species whose presence is key to maintaining biodiversity in an 
ecosystem and to upholding an ecological community’s structure 


mimicry 
an adaptation in which an organism looks like another organism that is 


dangerous, toxic, or distasteful to its predators 


mutualism 


a symbiotic relationship between two species where both species 
benefit 


parasite 
an organism that uses resources from another species: the host 


pioneer species 
the first species to appear in primary and secondary succession 


primary succession 
the succession on land that previously has had no life 


relative species abundance 
the absolute population size of a particular species relative to the 
population size of other species within the community 


secondary succession 
the succession in response to environmental disturbances that move a 
community away from its equilibrium 


species richness 
the number of different species in a community 


Discovering How Populations Change EnBio 
By the end of this section, you will be able to: 


e Explain how Darwin’s theory of evolution differed from the current 
view at the time 

e Describe how the present-day theory of evolution was developed 

e Describe how population genetics is used to study the evolution of 
populations 


The theory of evolution by natural selection describes a mechanism for 
species change over time. That species change had been suggested and 
debated well before Darwin. The view that species were static and 
unchanging was grounded in the writings of Plato, yet there were also 
ancient Greeks that expressed evolutionary ideas. 


In the early nineteenth century, Jean-Baptiste Lamarck published a book 
that detailed a mechanism for evolutionary change that is now referred to as 
inheritance of acquired characteristics. In Lamarck’s theory, 
modifications in an individual caused by its environment, or the use or 
disuse of a structure during its lifetime, could be inherited by its offspring 
and, thus, bring about change in a species. While this mechanism for 
evolutionary change as described by Lamarck was discredited, Lamarck’s 
ideas were an important influence on evolutionary thought. The inscription 
on the statue of Lamarck that stands at the gates of the Jardin des Plantes in 
Paris describes him as the “founder of the doctrine of evolution.” 


Charles Darwin and Natural Selection 


The actual mechanism for evolution was independently conceived of and 
described by two naturalists, Charles Darwin and Alfred Russell Wallace, in 
the mid-nineteenth century. Importantly, each spent time exploring the 
natural world on expeditions to the tropics. From 1831 to 1836, Darwin 
traveled around the world on H.M.S. Beagle, visiting South America, 
Australia, and the southern tip of Africa. Wallace traveled to Brazil to 
collect insects in the Amazon rainforest from 1848 to 1852 and to the 
Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s 
later journeys in the Malay Archipelago, included stops at several island 


chains, the last being the Galapagos Islands (west of Ecuador). On these 
islands, Darwin observed species of organisms on different islands that 
were clearly similar, yet had distinct differences. For example, the ground 
finches inhabiting the Galapagos Islands comprised several species that 
each had a unique beak shape ([link]). He observed both that these finches 
closely resembled another finch species on the mainland of South America 
and that the group of species in the Galapagos formed a graded series of 
beak sizes and shapes, with very small differences between the most 
similar. Darwin imagined that the island species might be all species 
modified from one original mainland species. In 1860, he wrote, “Seeing 
this gradation and diversity of structure in one small, intimately related 
group of birds, one might really fancy that from an original paucity of birds 
in this archipelago, one species had been taken and modified for different 
ends, aaa 

Charles Darwin, Journal of Researches into the Natural History and 
Geology of the Countries Visited during the Voyage of H.M.S. Beagle Round 
the World, under the Command of Capt. Fitz Roy, R.N, 2nd. ed. (London: 
John Murray, 1860), http://www.archive.org/details/journalofresea0Odarw. 


1. Geospiza magnirostris 2. Geospiza fortis 
3. Geospiza parvula 4. Certhidea olivacea 


Finches from Galapagos Archipelago 


Darwin observed that beak shape 
varies among finch species. He 
postulated that the beak of an 


ancestral species had adapted over 
time to equip the finches to 
acquire different food sources. 
This illustration shows the beak 
shapes for four species of ground 
finch: 1. Geospiza magnirostris 
(the large ground finch), 2. G. 
fortis (the medium ground finch), 
3. G. parvula (the small tree 
finch), and 4. Certhidea olivacea 
(the green-warbler finch). 


Wallace and Darwin both observed similar patterns in other organisms and 
independently conceived a mechanism to explain how and why such 
changes could take place. Darwin called this mechanism natural selection. 
Natural selection, Darwin argued, was an inevitable outcome of three 
principles that operated in nature. First, the characteristics of organisms are 
inherited, or passed from parent to offspring. Second, more offspring are 
produced than are able to survive; in other words, resources for survival and 
reproduction are limited. The capacity for reproduction in all organisms 
outstrips the availability of resources to support their numbers. Thus, there 
is a competition for those resources in each generation. Both Darwin and 
Wallace’s understanding of this principle came from reading an essay by the 
economist Thomas Malthus, who discussed this principle in relation to 
human populations. Third, offspring vary among each other in regard to 
their characteristics and those variations are inherited. Out of these three 
principles, Darwin and Wallace reasoned that offspring with inherited 
characteristics that allow them to best compete for limited resources will 
survive and have more offspring than those individuals with variations that 
are less able to compete. Because characteristics are inherited, these traits 
will be better represented in the next generation. This will lead to change in 
populations over generations in a process that Darwin called “descent with 
modification.” 


Papers by Darwin and Wallace ({link]) presenting the idea of natural 
selection were read together in 1858 before the Linnaean Society in 
London. The following year Darwin’s book, On the Origin of Species, was 
published, which outlined in considerable detail his arguments for evolution 
by natural selection. 


(a) Charles Darwin and (b) Alfred Wallace 
wrote scientific papers on natural selection that 
were presented together before the Linnean 
Society in 1858. 


Demonstrations of evolution by natural selection can be time consuming. 
One of the best demonstrations has been in the very birds that helped to 
inspire the theory, the Galapagos finches. Peter and Rosemary Grant and 
their colleagues have studied Galapagos finch populations every year since 
1976 and have provided important demonstrations of the operation of 
natural selection. The Grants found changes from one generation to the next 
in the beak shapes of the medium ground finches on the Galapagos island of 
Daphne Major. The medium ground finch feeds on seeds. The birds have 
inherited variation in the bill shape with some individuals having wide, 
deep bills and others having thinner bills. Large-billed birds feed more 
efficiently on large, hard seeds, whereas smaller billed birds feed more 


efficiently on small, soft seeds. During 1977, a drought period altered 
vegetation on the island. After this period, the number of seeds declined 
dramatically: the decline in small, soft seeds was greater than the decline in 
large, hard seeds. The large-billed birds were able to survive better than the 
small-billed birds the following year. The year following the drought when 
the Grants measured beak sizes in the much-reduced population, they found 
that the average bill size was larger ({link]). This was clear evidence for 
natural selection (differences in survival) of bill size caused by the 
availability of seeds. The Grants had studied the inheritance of bill sizes and 
knew that the surviving large-billed birds would tend to produce offspring 
with larger bills, so the selection would lead to evolution of bill size. 
Subsequent studies by the Grants have demonstrated selection on and 
evolution of bill size in this species in response to changing conditions on 
the island. The evolution has occurred both to larger bills, as in this case, 
and to smaller bills when large seeds became rare. 


Mean beak depth ——>"' 1978 Survivors 
Total number 
of birds = 90 


Mean beak depth —>} All Daphne birds 
' 1976 


Total number 
of birds = 751 


Percentage individuals 
in each depth class 
foe} 

Drought in 1977 


9 10 11 £12 13 14 6 7 8 9 10 11 £12 13 «14 
Beak depth (mm) | al |] Beak depth (mm) S 


A drought on the Galapagos island of Daphne Major in 1977 
reduced the number of small seeds available to finches, causing 
many of the small-beaked finches to die. This caused an increase 
in the finches’ average beak size between 1976 and 1978. 


Variation and Adaptation 


Natural selection can only take place if there is variation, or differences, 
among individuals in a population. Importantly, these differences must have 
some genetic basis; otherwise, selection will not lead to change in the next 
generation. This is critical because variation among individuals can be 
caused by non-genetic reasons, such as an individual being taller because of 
better nutrition rather than different genes. 


Genetic diversity in a population comes from two main sources: mutation 
and sexual reproduction. Mutation, a change in DNA, is the ultimate source 
of new alleles or new genetic variation in any population. An individual that 
has a mutated gene might have a different trait than other individuals in the 
population. However, this is not always the case. A mutation can have one 
of three outcomes on the organisms’ appearance (or phenotype): 


e A mutation may affect the phenotype of the organism in a way that 
gives it reduced fitness—lower likelihood of survival, resulting in 
fewer offspring. 

e A mutation may produce a phenotype with a beneficial effect on 
fitness. 

e Many mutations, called neutral mutations, will have no effect on 
fitness. 


A heritable trait that aids the survival and reproduction of an organism in its 
present environment is called an adaptation. An adaptation is a “match” of 
the organism to the environment. Adaptation to an environment comes 
about when a change in the range of genetic variation occurs over time that 
increases or maintains the match of the population with its environment. 
The variations in finch beaks shifted from generation to generation 
providing adaptation to food availability. 


Whether or not a trait is favorable depends on the environment at the time. 
The same traits do not always have the same relative benefit or 
disadvantage because environmental conditions can change. For example, 
finches with large bills were benefited in one climate, while small bills were 
a disadvantage; in a different climate, the relationship reversed. 


The Modern Synthesis 


The mechanisms of inheritance, genetics, were not understood at the time 
Darwin and Wallace were developing their idea of natural selection. This 
lack of understanding was a stumbling block to comprehending many 
aspects of evolution. In fact, blending inheritance was the predominant (and 
incorrect) genetic theory of the time, which made it difficult to understand 
how natural selection might operate. Darwin and Wallace were unaware of 
the genetics work by Austrian monk Gregor Mendel, which was published 
in 1866, not long after publication of On the Origin of Species. Mendel’s 
work was rediscovered in the early twentieth century at which time 
geneticists were rapidly coming to an understanding of the basics of 
inheritance. Initially, the newly discovered particulate nature of genes made 
it difficult for biologists to understand how gradual evolution could occur. 
But over the next few decades genetics and evolution were integrated in 
what became known as the modern synthesis—the coherent understanding 
of the relationship between natural selection and genetics that took shape by 
the 1940s and is generally accepted today. In sum, the modern synthesis 
describes how evolutionary pressures, such as natural selection, can affect a 
population’s genetic makeup, and, in turn, how this can result in the gradual 
evolution of populations and species. 


Population Genetics 


Recall that a gene for a particular character may have several variants, or 
alleles, that code for different traits associated with that character. For 
example, in the ABO blood type system in humans, three alleles determine 
the particular blood-type protein on the surface of red blood cells. Each 
individual in a population of diploid organisms can only carry two alleles 
for a particular gene, but more than two may be present in the individuals 
that make up the population. Mendel followed alleles as they were inherited 
from parent to offspring. In the early twentieth century, biologists began to 
study what happens to all the alleles in a population in a field of study 
known as population genetics. 


Until now, we have defined evolution as a change in the characteristics of a 
population of organisms, but behind that phenotypic change is genetic 
change. In population genetic terms, evolution is defined as a change in the 
frequency of an allele in a population. 


There are several ways the allele frequencies of a population can change. 
One of those ways is natural selection. If a given allele confers a phenotype 
that allows an individual to have more offspring that survive and reproduce, 
that allele, by virtue of being inherited by those offspring, will be in greater 
frequency in the next generation. Since allele frequencies always add up to 
100 percent, an increase in the frequency of one allele always means a 
corresponding decrease in one or more of the other alleles. Highly 
beneficial alleles may, over a very few generations, become “fixed” in this 
way, Meaning that every individual of the population will carry the allele. 
Similarly, detrimental alleles may be swiftly eliminated from the gene pool, 
the sum of all the alleles in a population. Part of the study of population 
genetics is tracking how selective forces change the allele frequencies in a 
population over time, which can give scientists clues regarding the selective 
forces that may be operating on a given population. The studies of changes 
in wing coloration in the peppered moth from mottled white to dark in 
response to soot-covered tree trunks and then back to mottled white when 
factories stopped producing so much soot is a classic example of studying 
evolution in natural populations ([link]). 


Light-colored peppered moths are 
better camouflaged against a 
pristine environment; likewise, 
dark-colored peppered moths are 
better camouflaged against a sooty 
environment. Thus, as the Industrial 
Revolution progressed in 
nineteenth-century England, the 
color of the moth population shifted 
from light to dark. 


Population after 
natural selection 


Original 
population 


As the Industrial Revolution caused trees to darken 
from soot, darker colored peppered moths were 
better camouflaged than the lighter colored ones, 
which caused there to be more of the darker 
colored moths in the population. 


In the early twentieth century, English mathematician Godfrey Hardy and 
German physician Wilhelm Weinberg independently provided an 
explanation for a somewhat counterintuitive concept. Hardy’s original 
explanation was in response to a misunderstanding as to why a “dominant” 
allele, one that masks a recessive allele, should not increase in frequency in 
a population until it eliminated all the other alleles. The question resulted 
from a common confusion about what “dominant” means, but it forced 
Hardy, who was not even a biologist, to point out that if there are no factors 
that affect an allele frequency those frequencies will remain constant from 
one generation to the next. This principle is now known as the Hardy- 
Weinberg equilibrium. The theory states that a population’s allele and 
genotype frequencies are inherently stable—unless some kind of 
evolutionary force is acting on the population, the population would carry 
the same alleles in the same proportions generation after generation. The 
four most important evolutionary forces, which will disrupt the equilibrium, 
are natural selection, mutation, genetic drift, and migration into or out of a 
population. If an allele is favored by natural selection, it will increase in 
frequency. Genetic drift causes random changes in allele frequencies when 
populations are small. Genetic drift can often be important in evolution, as 
discussed in the next section. Finally, if two populations of a species have 
different allele frequencies, migration of individuals between them will 
cause frequency changes in both populations. As it happens, there is no 
population in which one or more of these processes are not operating, so 
populations are always evolving, and the Hardy-Weinberg equilibrium will 
never be exactly observed. However, the Hardy-Weinberg principle gives 
scientists a baseline expectation for allele frequencies in a non-evolving 
population to which they can compare evolving populations and thereby 
infer what evolutionary forces might be at play. The population is evolving 
if the frequencies of alleles or genotypes deviate from the value expected 
from the Hardy-Weinberg principle. 


Section Summary 


Evolution by natural selection arises from three conditions: individuals 
within a species vary, some of those variations are heritable, and organisms 
have more offspring than resources can support. The consequence is that 
individuals with relatively advantageous variations will be more likely to 


survive and have higher reproductive rates than those individuals with 
different traits. The advantageous traits will be passed on to offspring in 
greater proportion. Thus, the trait will have higher representation in the next 
and subsequent generations leading to genetic change in the population. 


The modern synthesis of evolutionary theory grew out of the reconciliation 
of Darwin’s, Wallace’s, and Mendel’s thoughts on evolution and heredity. 
Population genetics is a theoretical framework for describing evolutionary 
change in populations through the change in allele frequencies. Population 
genetics defines evolution as a change in allele frequency over generations. 
In the absence of evolutionary forces allele frequencies will not change in a 
population; this is known as Hardy-Weinberg equilibrium principle. 
However, in all populations, mutation, natural selection, genetic drift, and 
migration act to change allele frequencies. 


Glossary 


adaptation 
a heritable trait or behavior in an organism that aids in its survival in 
its present environment 


analogous structure 
a structure that is similar because of evolution in response to similar 
selection pressures resulting in convergent evolution, not similar 
because of descent from a common ancestor 


convergent evolution 
an evolution that results in similar forms on different species 


divergent evolution 
an evolution that results in different forms in two species with a 
common ancestor 


gene pool 
all of the alleles carried by all of the individuals in the population 


genetic drift 
the effect of chance on a population’s gene pool 


homologous structure 
a structure that is similar because of descent from a common ancestor 


inheritance of acquired characteristics 
a phrase that describes the mechanism of evolution proposed by 
Lamarck in which traits acquired by individuals through use or disuse 
could be passed on to their offspring thus leading to evolutionary 
change in the population 


macroevolution 
a broader scale of evolutionary changes seen over paleontological time 


microevolution 
the changes in a population’s genetic structure (i.e., allele frequency) 


migration 
the movement of individuals of a population to a new location; in 
population genetics it refers to the movement of individuals and their 
alleles from one population to another, potentially changing allele 
frequencies in both the old and the new population 


modern synthesis 
the overarching evolutionary paradigm that took shape by the 1940s 
and is generally accepted today 


natural selection 
the greater relative survival and reproduction of individuals in a 
population that have favorable heritable traits, leading to evolutionary 
change 


population genetics 
the study of how selective forces change the allele frequencies in a 
population over time 


variation 
the variety of alleles in a population 


DNA Replication EnBio 
By the end of this section, you will be able to: 


e Explain the process of DNA replication 


When a cell divides, it is important that each daughter cell receives an 
identical copy of the DNA. This is accomplished by the process of DNA 
replication. 


The elucidation of the structure of the double helix provided a hint as to 
how DNA is copied. Recall that adenine nucleotides pair with thymine 
nucleotides, and cytosine with guanine. This means that the two strands are 
complementary to each other. For example, a strand of DNA witha 
nucleotide sequence of AGTCATGA will have a complementary strand 
with the sequence TCAGTACT #((link]). 

3 


a] a a 


The two strands of DNA are 
complementary, meaning the sequence of 


bases in one strand can be used to create the 
correct sequence of bases in the other strand. 


Because of the complementarity of the two strands, having one strand 
means that it is possible to recreate the other strand. This model for 
replication suggests that the two strands of the double helix separate during 
replication, and each strand serves as a template from which the new 
complementary strand is copied ((Link]). 


Semi-conservative model of DNA Replication 


The semiconservative model of 
DNA replication is shown. Gray 
indicates the original DNA 
strands, and blue indicates newly 
synthesized DNA. 


During DNA replication, each of the two strands that make up the double 
helix serves as a template from which new strands are copied. The new 
strand will be complementary to the parental or “old” strand. Each new 


double strand consists of one parental strand and one new daughter strand. 
This is known as semiconservative replication. When two DNA copies are 
formed, they have an identical sequence of nucleotide bases and are divided 
equally into two daughter cells. 


Glossary 


DNA ligase 
the enzyme that catalyzes the joining of DNA fragments together 


DNA polymerase 
an enzyme that synthesizes a new strand of DNA complementary to a 
template strand 


helicase 
an enzyme that helps to open up the DNA helix during DNA 
replication by breaking the hydrogen bonds 


lagging strand 
during replication of the 3' to 5' strand, the strand that is replicated in 
short fragments and away from the replication fork 


leading strand 
the strand that is synthesized continuously in the 5' to 3' direction that 
is synthesized in the direction of the replication fork 


mismatch repair 
a form of DNA repair in which non-complementary nucleotides are 
recognized, excised, and replaced with correct nucleotides 


mutation 
a permanent variation in the nucleotide sequence of a genome 


nucleotide excision repair 
a form of DNA repair in which the DNA molecule is unwound and 
separated in the region of the nucleotide damage, the damaged 
nucleotides are removed and replaced with new nucleotides using the 


complementary strand, and the DNA strand is resealed and allowed to 
rejoin its complement 


Okazaki fragments 
the DNA fragments that are synthesized in short stretches on the 
lagging strand 


primer 
a short stretch of RNA nucleotides that is required to initiate 
replication and allow DNA polymerase to bind and begin replication 


replication fork 
the Y-shaped structure formed during the initiation of replication 


semiconservative replication 
the method used to replicate DNA in which the double-stranded 
molecule is separated and each strand acts as a template for a new 
strand to be synthesized, so the resulting DNA molecules are 
composed of one new strand of nucleotides and one old strand of 
nucleotides 


telomerase 
an enzyme that contains a catalytic part and an inbuilt RNA template; 
it functions to maintain telomeres at chromosome ends 


telomere 
the DNA at the end of linear chromosomes 


Energy Flow through Ecosystems EnBio 
By the end of this section, you will be able to: 


e Describe the basic types of ecosystems on Earth 

¢ Differentiate between food chains and food webs and recognize the 
importance of each 

e Describe how organisms acquire energy in a food web and in 
associated food chains 

e Explain how the efficiency of energy transfers between trophic levels 
effects ecosystem 


An ecosystem is a community of living organisms and their abiotic (non- 
living) environment. Ecosystems can be small, such as the tide pools found 
near the rocky shores of many oceans, or large, such as those found in the 
tropical rainforest of the Amazon in Brazil ([link]). 


(a) (b) 


A (a) tidal pool ecosystem in Matinicus Island, Maine, is 
a small ecosystem, while the (b) Amazon rainforest in 
Brazil is a large ecosystem. (credit a: modification of 
work by Jim Kuhn; credit b: modification of work by 

Ivan Mlinaric) 


There are three broad categories of ecosystems based on their general 
environment: freshwater, marine, and terrestrial. Within these three 


categories are individual ecosystem types based on the environmental 
habitat and organisms present. 


Ecology of Ecosystems 


Life in an ecosystem often involves competition for limited resources, 
which occurs both within a single species and between different species. 
Organisms compete for food, water, sunlight, space, and mineral nutrients. 
These resources provide the energy for metabolic processes and the matter 
to make up organisms’ physical structures. Other critical factors influencing 
community dynamics are the components of its physical environment: a 
habitat’s climate (seasons, sunlight, and rainfall), elevation, and soil/rocks. 
These can all be important environmental variables that determine which 
organisms can exist within a particular area. 


Freshwater ecosystems are the least common, occurring on only 1.8 percent 
of Earth's surface. These systems comprise lakes, rivers, streams, and 
springs; they are quite diverse, and support a variety of animals, plants, 
fungi, protists and prokaryotes. 


Marine ecosystems are the most common, comprising 75 percent of Earth's 
surface and consisting of three basic types: shallow ocean, deep ocean 
water, and deep ocean bottom. Shallow ocean ecosystems include extremely 
biodiverse coral reef ecosystems, yet the deep ocean water is known for 
large numbers of plankton and krill (small crustaceans) that support it. 
These two environments are especially important to aerobic respirators 
worldwide, as the phytoplankton perform 40 percent of all photosynthesis 
on Earth. Although not as diverse as the other two, deep ocean bottom 
ecosystems contain a wide variety of marine organisms. Such ecosystems 
exist even at depths where light is unable to penetrate through the water. 


Terrestrial ecosystems, also known for their diversity, are grouped into large 
categories called biomes. A biome is a large-scale community of 
organisms, primarily defined on land by the dominant plant types that exist 
in geographic regions of the planet with similar climatic conditions. 
Examples of biomes include tropical rainforests, savannas, deserts, 
grasslands, temperate forests, and tundras. Grouping these ecosystems into 


just a few biome categories obscures the great diversity of the individual 
ecosystems within them. For example, the saguaro cacti (Carnegiea 
gigantean) and other plant life in the Sonoran Desert, in the United States, 
are relatively diverse compared with the desolate rocky desert of Boa Vista, 
an island off the coast of Western Africa ([link]). 


(a) (b) 


Desert ecosystems, like all ecosystems, can vary greatly. 
The desert in (a) Saguaro National Park, Arizona, has 
abundant plant life, while the rocky desert of (b) Boa Vista 
island, Cape Verde, Africa, is devoid of plant life. (credit a: 
modification of work by Jay Galvin; credit b: modification 
of work by Ingo Woélberm) 


Ecosystems and Disturbance 


Ecosystems are complex with many interacting parts. They are routinely 
exposed to various disturbances: changes in the environment that affect 
their compositions, such as yearly variations in rainfall and temperature. 
Many disturbances are a result of natural processes. The impact of 
environmental disturbances caused by human activities is now as significant 
as the changes wrought by natural processes. Human agricultural practices, 


air pollution, acid rain, global deforestation, overfishing, oil spills, and 
illegal dumping on land and into the ocean all have impacts on ecosystems. 


Food Chains and Food Webs 


A food chain is a linear sequence of organisms through which nutrients and 
energy pass as one organism eats another; the levels in the food chain are 
producers, primary consumers, higher-level consumers, and finally 
decomposers. These levels are used to describe ecosystem structure and 
dynamics. There is a single path through a food chain. Each organism in a 
food chain occupies a specific trophic level (energy level), its position in 
the food chain or food web. 


In many ecosystems, the base, or foundation, of the food chain consists of 
photosynthetic organisms (plants or phytoplankton), which are called 
producers. The organisms that consume the producers are herbivores: the 
primary consumers. Secondary consumers are usually carnivores that eat 
the primary consumers. Tertiary consumers are carnivores that eat other 
carnivores. Higher-level consumers feed on the next lower trophic levels, 
and so on, up to the organisms at the top of the food chain: the apex 
consumers. In the Lake Ontario food chain, shown in [link], the Chinook 
salmon is the apex consumer at the top of this food chain. 


ORGANISM TROPHIC LEVEL 


Slimy sculpin 


Mollusks oe | 
| 
Green algae 


These are the trophic levels 
of a food chain in Lake 
Ontario at the United States— 
Canada border. Energy and 
nutrients flow from 
photosynthetic green algae at 
the base to the top of the food 
chain: the Chinook salmon. 
(credit: modification of work 
by National Oceanic and 
Atmospheric 
Administration/NOAA) 


One major factor that limits the number of steps in a food chain is energy. 
Energy is lost at each trophic level and between trophic levels as heat and in 
the transfer to decomposers ({link]). Thus, after a limited number of trophic 
energy transfers, the amount of energy remaining in the food chain may not 
be great enough to support viable populations at yet a higher trophic level. 


Producers 
Diatoms, water lettuce, 
arrowhead, eel grass 


Primary consumers 
Red-bellied turtle, Florida 
apple snail, flathead mullet, 
midge larvae 


Secondary consumers 
Killifish, bluegill sunfish, 
whirligig beetle, 

water strider 


Tertiary consumers 
Bass, gar, water snake 


5,000 10,000 15,000 
Energy content (kcal/m2/yr) 


The relative energy in trophic levels in a Silver Springs, 

Florida, ecosystem is shown. Each trophic level has less 

energy available, and usually, but not always, supports a 
smaller mass of organisms at the next level. 


There is a one problem when using food chains to describe most 
ecosystems. Even when all organisms are grouped into appropriate trophic 
levels, some of these organisms can feed on more than one trophic level; 


likewise, some of these organisms can also be fed on from multiple trophic 
levels. In addition, species feed on and are eaten by more than one species. 
In other words, the linear model of ecosystems, the food chain, is a 
hypothetical, overly simplistic representation of ecosystem structure. A 
holistic model—which includes all the interactions between different 
species and their complex interconnected relationships with each other and 
with the environment—is a more accurate and descriptive model for 
ecosystems. A food web is a concept that accounts for the multiple trophic 
(feeding) interactions between each species and the many species it may 
feed on, or that feed on it. The matter and energy movements of virtually all 
ecosystems are more accurately described by food webs ((link]). 


This food web shows the interactions between 
organisms across trophic levels. Arrows point 
from an organism that is consumed to the 


organism that consumes it. All the producers 
and consumers eventually become nourishment 
for the decomposers (fungi, mold, earthworms, 
and bacteria in the soil). (credit "fox": 
modification of work by Kevin Bacher, NPS; 
credit "owl": modification of work by John and 
Karen Hollingsworth, USFWS; credit "snake": 
modification of work by Steve Jurvetson; 
credit "robin": modification of work by Alan 
Vernon; credit "frog": modification of work by 
Alessandro Catenazzi; credit "spider": 
modification of work by "Sanba38"/Wikimedia 
Commons; credit "centipede": modification of 
work by “Bauerph”/Wikimedia Commons; 
credit "squirrel": modification of work by 
Dawn Huczek; credit "mouse": modification of 
work by NIGMS, NIH; credit "sparrow": 
modification of work by David Friel; credit 
"beetle": modification of work by Scott Bauer, 
USDA Agricultural Research Service; credit 
"mushrooms": modification of work by Chris 
Wee; credit "mold": modification of work by 
Dr. Lucille Georg, CDC; credit "earthworm": 
modification of work by Rob Hille; credit 
"bacteria": modification of work by Don 
Stalons, CDC) 


Note: 
Concept in Action 


OR eae 
cent ee 
—_— ' 

4 openstax COLLEGE 


[el Mae are 


Head to this online interactive simulator to investigate food web function. 
In the Interactive Labs box, under Food Web, click Step 1. Read the 
instructions first, and then click Step 2 for additional instructions. When 
you are ready to create a simulation, in the upper-right corner of the 
Interactive Labs box, click OPEN SIMULATOR. 


Another trophic level are the decomposers, organisms that feed on decaying 
organic matter (dead organisms, parts of organisms and wastes). Some 
decomposers are called detritivores which consume organic detritus. These 
organisms are usually bacteria, fungi, and invertebrate animals that recycle 
organic material back into the biotic part of the ecosystem as they 
themselves are consumed by other organisms. 


How Organisms Acquire Energy in a Food Web 


All living things require energy in one form or another. Energy is used by 
most complex metabolic pathways (usually in the form of ATP), especially 
those responsible for building large molecules from smaller compounds. 
Living organisms would not be able to assemble macromolecules (proteins, 
lipids, nucleic acids, and complex carbohydrates) from their monomers 
without a constant energy input. 


Food-web diagrams illustrate how energy flows directionally through 
ecosystems. They can also indicate how efficiently organisms acquire 
energy, use it, and how much remains for use by other organisms of the 
food web. Energy is acquired by living things in two ways: autotrophs 
harness light or chemical energy and heterotrophs acquire energy through 
the consumption and digestion of other living or previously living 
organisms. 


Photosynthetic and chemosynthetic organisms are autotrophs, which are 
organisms capable of synthesizing their own food. Photosynthetic 
autotrophs (photoautotrophs) use sunlight as an energy source, and 
chemosynthetic autotrophs (chemoautotrophs) use inorganic molecules as 
an energy source. Autotrophs are critical for most ecosystems: they are the 
producer trophic level. Without these organisms, energy would not be 
available to other living organisms, and life itself would not be possible. 


Photoautotrophs, such as plants, algae, and photosynthetic bacteria, are the 
energy source for a majority of the world’s ecosystems. Photoautotrophs 
harness the Sun’s solar energy by converting it to chemical energy in the 
form of ATP (and NADP). The energy stored in ATP is used to synthesize 
complex organic molecules, such as glucose. The rate at which 
photosynthetic producers incorporate energy from the Sun is called gross 
primary productivity. However, not all of the energy incorporated by 
producers is available to the other organisms in the food web because 
producers must also grow and reproduce, which consumes energy. Net 
primary productivity is the energy that remains in the producers after 
accounting for these organisms’ respiration and heat loss. The net 
productivity is then available to the primary consumers at the next trophic 
level. 


Chemoautotrophs are primarily bacteria and archaea that are found in rare 
ecosystems where sunlight is not available, such as those associated with 
dark caves or hydrothermal vents at the bottom of the ocean ({link]). Many 
chemoautotrophs in hydrothermal vents use hydrogen sulfide (HS), which 
is released from the vents as a source of chemical energy; this allows them 
to synthesize complex organic molecules, such as glucose, for their own 
energy and, in turn, supplies energy to the rest of the ecosystem. 


Swimming shrimp, a few squat lobsters, and 
hundreds of vent mussels are seen at a 
hydrothermal vent at the bottom of the 
ocean. As no sunlight penetrates to this 

depth, the ecosystem is supported by 
chemoautotrophic bacteria and organic 
material that sinks from the ocean’s surface. 
This picture was taken in 2006 at the 
submerged NW Eifuku volcano off the coast 
of Japan by the National Oceanic and 
Atmospheric Administration (NOAA). The 
summit of this highly active volcano lies 
1535 m below the surface. 


Consequences of Food Webs: Biological Magnification 


One of the most important consequences of ecosystem dynamics in terms of 
human impact is biomagnification. Biomagnification is the increasing 
concentration of persistent, toxic substances in organisms at each successive 
trophic level. These are substances that are fat soluble, not water soluble, 


and are stored in the fat reserves of each organism. Many substances have 
been shown to biomagnify, including classical studies with the pesticide 
dichlorodiphenyltrichloroethane (DDT), which were described in the 1960s 
bestseller, Silent Spring by Rachel Carson. DDT was a commonly used 
pesticide before its dangers to apex consumers, such as the bald eagle, 
became known. In aquatic ecosystems, organisms from each trophic level 
consumed many organisms in the lower level, which caused DDT to 
increase in birds (apex consumers) that ate fish. Thus, the birds 
accumulated sufficient amounts of DDT to cause fragility in their eggshells. 
This effect increased egg breakage during nesting and was shown to have 
devastating effects on these bird populations. The use of DDT was banned 
in the United States in the 1970s. 


Other substances that biomagnify are polychlorinated biphenyls (PCB), 
which were used as coolant liquids in the United States until their use was 
banned in 1979, and heavy metals, such as mercury, lead, and cadmium. 
These substances are best studied in aquatic ecosystems, where predatory 
fish species accumulate very high concentrations of toxic substances that 
are at quite low concentrations in the environment and in producers. As 
illustrated in a study performed by the NOAA in the Saginaw Bay of Lake 
Huron of the North American Great Lakes ([link]), PCB concentrations 
increased from the producers of the ecosystem (phytoplankton) through the 
different trophic levels of fish species. The apex consumer, the walleye, has 
more than four times the amount of PCBs compared to phytoplankton. 
Also, based on results from other studies, birds that eat these fish may have 
PCB levels at least one order of magnitude higher than those found in the 
lake fish. 


 : 
Rainbow Smelt / 


Yellow 
Perch 
es w@ 


Alewife calls 


White Sucker 


This chart shows the PCB 
concentrations found at the various 
trophic levels in the Saginaw Bay 
ecosystem of Lake Huron. Notice that 
the fish in the higher trophic levels 
accumulate more PCBs than those in 
lower trophic levels. (credit: Patricia 
Van Hoof, NOAA) 


Other concerns have been raised by the biomagnification of heavy metals, 
such as mercury and cadmium, in certain types of seafood. The United 
States Environmental Protection Agency recommends that pregnant women 
and young children should not consume any swordfish, shark, king 
mackerel, or tilefish because of their high mercury content. These 
individuals are advised to eat fish low in mercury: salmon, shrimp, pollock, 
and catfish. Biomagnification is a good example of how ecosystem 
dynamics can affect our everyday lives, even influencing the food we eat. 


Section Summary 


Ecosystems exist underground, on land, at sea, and in the air. Organisms in 
an ecosystem acquire energy in a variety of ways, which is transferred 
between trophic levels as the energy flows from the base to the top of the 
food web, with energy being lost at each transfer. There is energy lost at 
each trophic level, so the lengths of food chains are limited because there is 
a point where not enough energy remains to support a population of 
consumers. Fat soluble compounds biomagnify up a food chain causing 
damage to top consumers. even when environmental concentrations of a 
toxin are low. 


Glossary 


autotroph 
an organism capable of synthesizing its own food molecules from 
smaller inorganic molecules 


apex consumer 
an organism at the top of the food chain 


biomagnification 
an increasing concentration of persistent, toxic substances in 
organisms at each trophic level, from the producers to the apex 
consumers 


biome 
a large-scale community of organisms, primarily defined on land by 
the dominant plant types that exist in geographic regions of the planet 
with similar climatic conditions 


chemoautotroph 
an organism capable of synthesizing its own food using energy from 
inorganic molecules 


detrital food web 
a type of food web that is supported by dead or decaying organisms 
rather than by living autotrophs; these are often associated with 
grazing food webs within the same ecosystem 


ecosystem 
a community of living organisms and their interactions with their 
abiotic environment 


equilibrium 
the steady state of a system in which the relationships between 
elements of the system do not change 


food chain 
a linear sequence of trophic (feeding) relationships of producers, 
primary consumers, and higher level consumers 


food web 
a web of trophic (feeding) relationships among producers, primary 
consumers, and higher level consumers in an ecosystem 


grazing food web 
a type of food web in which the producers are either plants on land or 
phytoplankton in the water; often associated with a detrital food web 
within the same ecosystem 


gross primary productivity 
the rate at which photosynthetic producers incorporate energy from the 
Sun 


net primary productivity 
the energy that remains in the producers after accounting for the 
organisms’ respiration and heat loss 


photoautotroph 
an organism that uses sunlight as an energy source to synthesize its 
own food molecules 


primary consumer 
the trophic level that obtains its energy from the producers of an 


ecosystem 


producer 


the trophic level that obtains its energy from sunlight, inorganic 
chemicals, or dead or decaying organic material 


resilience (ecological) 
the speed at which an ecosystem recovers equilibrium after being 
disturbed 


resistance (ecological) 
the ability of an ecosystem to remain at equilibrium in spite of 
disturbances 


secondary consumer 
a trophic level in an ecosystem, usually a carnivore that eats a primary 
consumer 


tertiary consumer 
a trophic level in an ecosystem, usually carnivores that eat other 
carnivores 


trophic level 
the position of a species or group of species in a food chain or a food 
web 


Evidence of Evolution EnBio 
By the end of this section, you will be able to: 


e Explain sources of evidence for evolution 
e Define homologous and vestigial structures 


The evidence for evolution is compelling and extensive. Looking at every 
level of organization in living systems, biologists see the signature of past 
and present evolution. Darwin dedicated a large portion of his book, On the 
Origin of Species, identifying patterns in nature that were consistent with 
evolution and since Darwin our understanding has become clearer and 
broader. 


Fossils 


Fossils provide solid evidence that organisms from the past are not the same 
as those found today; fossils show a progression of evolution. Scientists 
determine the age of fossils and categorize them all over the world to 
determine when the organisms lived relative to each other. The resulting 
fossil record tells the story of the past, and shows the evolution of form over 
millions of years ({link]). For example, highly detailed fossil records have 
been recovered for sequences of species in the evolution of whales and 
modern horses. The fossil record of horses in North America is especially 
rich and many contain transition fossils: those showing intermediate 
anatomy between earlier and later forms. The fossil record extends back to 
a dog-like ancestor some 55 million years ago that gave rise to the first 
horse-like species 55 to 42 million years ago in the genus Eohippus. The 
series of fossils tracks the change in anatomy resulting from a gradual 
drying trend that changed the landscape from a forested one to a prairie. 
Successive fossils show the evolution of teeth shapes and foot and leg 
anatomy to a grazing habit, with adaptations for escaping predators, for 
example in species of Mesohippus found from 40 to 30 million years ago. 
Later species showed gains in size, such as those of Hipparion, which 
existed from about 23 to 2 million years ago. 


Eohippus Mesohippus Hipparion Przewalski horse 


55-45 million years ago 40-30 million years ago 23-2 million years ago recent 
"vr SS A. 2 
55 million 


years ago Today 


This illustration shows an artist’s renderings of these species 
derived from fossils of the evolutionary history of the horse and its 
ancestors. The species depicted are only four from a very diverse 
lineage that contains many branches, dead ends, and adaptive 
radiations. One of the trends, depicted here is the evolutionary 
tracking of a drying climate and increase in prairie versus forest 
habitat reflected in forms that are more adapted to grazing and 
predator escape through running. Przewalski's horse is one of a 
few living species of horse. 


Anatomy and Embryology 


Another type of evidence for evolution is the presence of structures in 
organisms that share the same basic form. For example, the bones in the 
appendages of a human, dog, bird, and whale all share the same overall 
construction ([link]). That similarity results from their origin in the 
appendages of a common ancestor. Over time, evolution led to changes in 
the shapes and sizes of these bones in different species, but they have 
maintained the same overall layout, evidence of descent from a common 
ancestor. Scientists call these synonymous parts homologous structures. 


Some structures exist in organisms that have no apparent function at all, and 


appear to be residual parts from a past ancestor. For example, some snakes 
have pelvic bones despite having no legs because they descended from 
reptiles that did have legs. These unused structures without function are 


called vestigial structures. Other examples of vestigial structures are wings 


on flightless birds (which may have other functions), leaves on some cacti, 
traces of pelvic bones in whales, and the sightless eyes of cave animals. 


Human Dog Bird Whale 


The similar construction of these 
appendages indicates that these 
organisms share a common 
ancestor. 


Note: 
Concept in Action 


Cher Real 
oe Picy 


=, 
meee OPENStAX COLLEGE 
” 


Click through the activities at this interactive site to guess which bone 
structures are homologous and which are analogous, and to see examples 
of all kinds of evolutionary adaptations that illustrate these concepts. 


Another evidence of evolution is the convergence of form in organisms that 
share similar environments. For example, species of unrelated animals, such 
as the arctic fox and ptarmigan (a bird), living in the arctic region have 
temporary white coverings during winter to blend with the snow and ice 
({link]). The similarity occurs not because of common ancestry, indeed one 
covering is of fur and the other of feathers, but because of similar selection 
pressures—the benefits of not being seen by predators. 


The white winter coat of (a) the arctic fox and 

(b) the ptarmigan’s plumage are adaptations to 

their environments. (credit a: modification of 
work by Keith Morehouse) 


Embryology, the study of the development of the anatomy of an organism 
to its adult form also provides evidence of relatedness between now widely 
divergent groups of organisms. Structures that are absent in some groups 
often appear in their embryonic forms and disappear by the time the adult or 
juvenile form is reached. For example, all vertebrate embryos, including 
humans, exhibit gill slits at some point in their early development. These 
disappear in the adults of terrestrial groups, but are maintained in adult 
forms of aquatic groups such as fish and some amphibians. Great ape 


embryos, including humans, have a tail structure during their development 
that is lost by the time of birth. The reason embryos of unrelated species are 
often similar is that mutational changes that affect the organism during 
embryonic development can cause amplified differences in the adult, even 
while the embryonic similarities are preserved. 


Biogeography 


The geographic distribution of organisms on the planet follows patterns that 
are best explained by evolution in conjunction with the movement of 
tectonic plates over geological time. Broad groups that evolved before the 
breakup of the supercontinent Pangaea (about 200 million years ago) are 
distributed worldwide. Groups that evolved since the breakup appear 
uniquely in regions of the planet, for example the unique flora and fauna of 
northern continents that formed from the supercontinent Laurasia and of the 
southern continents that formed from the supercontinent Gondwana. The 
presence of Proteaceae in Australia, southern Africa, and South America is 
best explained by the plant family’s presence there prior to the southern 
supercontinent Gondwana breaking up ((Link]). 


Proteacea flower [RR 
Banksia spinulosa 3% 


The Proteacea family of plants evolved before the supercontinent 
Gondwana broke up. Today, members of this plant family are 


found throughout the southern hemisphere (shown in red). (credit 
“Proteacea flower”: modification of work by “dorofofoto”/Flickr) 


The great diversification of the marsupials in Australia and the absence of 
other mammals reflects that island continent’s long isolation. Australia has 
an abundance of endemic species—species found nowhere else—which is 
typical of islands whose isolation by expanses of water prevents migration 
of species to other regions. Over time, these species diverge evolutionarily 
into new species that look very different from their ancestors that may exist 
on the mainland. The marsupials of Australia, the finches on the Galapagos, 
and many species on the Hawaiian Islands are all found nowhere else but on 
their island, yet display distant relationships to ancestral species on 
mainlands. 


Molecular Biology 


Like anatomical structures, the structures of the molecules of life reflect 
descent with modification. Evidence of a common ancestor for all of life is 
reflected in the universality of DNA as the genetic material and of the near 
universality of the genetic code and the machinery of DNA replication and 
expression. Fundamental divisions in life between the three domains are 
reflected in major structural differences in otherwise conservative structures 
such as the components of ribosomes and the structures of membranes. In 
general, the relatedness of groups of organisms is reflected in the similarity 
of their DNA sequences—exactly the pattern that would be expected from 
descent and diversification from a common ancestor. 


DNA sequences have also shed light on some of the mechanisms of 
evolution. For example, it is clear that the evolution of new functions for 
proteins commonly occurs after gene duplication events. These duplications 
are a kind of mutation in which an entire gene is added as an extra copy (or 
many copies) in the genome. These duplications allow the free modification 
of one copy by mutation, selection, and drift, while the second copy 
continues to produce a functional protein. This allows the original function 


for the protein to be kept, while evolutionary forces tweak the copy until it 
functions in a new way. 


Section Summary 


The evidence for evolution is found at all levels of organization in living 
things and in the extinct species we know about through fossils. Fossils 
provide evidence for the evolutionary change through now extinct forms 
that led to modern species. For example, there is a rich fossil record that 
shows the evolutionary transitions from horse ancestors to modern horses 
that document intermediate forms and a gradual adaptation o changing 
ecosystems. The anatomy of species and the embryological development of 
that anatomy reveal common structures in divergent lineages that have been 
modified over time by evolution. The geographical distribution of living 
species reflects the origins of species in particular geographic locations and 
the history of continental movements. The structures of molecules, like 
anatomical structures, reflect the relationships of living species and match 
patterns of similarity expected from descent with modification. 


Glossary 


vestigial structure 
a physical structure present in an organism but that has no apparent 
function and appears to be from a functional structure in a distant 
ancestor 


The Genome EnBio 
By the end of this section, you will be able to: 


e Describe the prokaryotic and eukaryotic genome 
e Distinguish between chromosomes, genes, and traits 


The continuity of life from one cell to another has its foundation in the 
reproduction of cells by way of the cell cycle. The cell cycle is an orderly 
sequence of events in the life of a cell from the division of a single parent 
cell to produce two new daughter cells, to the subsequent division of those 
daughter cells. The mechanisms involved in the cell cycle are highly 
conserved across eukaryotes. Organisms as diverse as protists, plants, and 
animals employ similar steps. 


Genomic DNA 


Before discussing the steps a cell undertakes to replicate, a deeper 
understanding of the structure and function of a cell’s genetic information is 
necessary. A cell’s complete complement of DNA is called its genome. In 
prokaryotes, the genome is composed of a single, double-stranded DNA 
molecule in the form of a loop or circle. The region in the cell containing 
this genetic material is called a nucleoid. Some prokaryotes also have 
smaller loops of DNA called plasmids that are not essential for normal 
growth. 


In eukaryotes, the genome comprises several double-stranded, linear DNA 
molecules ({link]) bound with proteins to form complexes called 
chromosomes. Each species of eukaryote has a characteristic number of 
chromosomes in the nuclei of its cells. Human body cells (somatic cells) 
have 46 chromosomes. A somatic cell contains two matched sets of 
chromosomes, a configuration known as diploid. The letter n is used to 
represent a single set of chromosomes; therefore a diploid organism is 
designated 2n. Human cells that contain one set of 23 chromosomes are 
called gametes, or sex cells; these eggs and sperm are designated n, or 
haploid. 


10 11 12 


ih 
16 17 18 


22 x 


There are 23 pairs of homologous 
chromosomes in a female human 
somatic cell. These chromosomes 
are viewed within the nucleus 
(top), removed from a cell in 
mitosis (right), and arranged 
according to length (left) in an 
arrangement called a karyotype. In 
this image, the chromosomes were 
exposed to fluorescent stains to 
distinguish them. (credit: “718 
Bot”/Wikimedia Commons, 
National Human Genome 
Research) 


The matched pairs of chromosomes in a diploid organism are called 
homologous chromosomes. Homologous chromosomes are the same 
length and have specific nucleotide segments called genes in exactly the 
same location, or locus. Genes, the functional units of chromosomes, 
determine specific characteristics by coding for specific proteins. Traits are 
the different forms of a characteristic. For example, the shape of earlobes is 
a characteristic with traits of free or attached. 


Each copy of the homologous pair of chromosomes originates from a 
different parent; therefore, the copies of each of the genes themselves may 
not be identical. The variation of individuals within a species is caused by 
the specific combination of the genes inherited from both parents. Minor 
variations in traits such as those for blood type, eye color, and height 
contribute to the natural variation found within a species. The sex 
chromosomes, X and Y, are the single exception to the rule of homologous 
chromosomes; other than a small amount of homology that is necessary to 
reliably produce gametes, the genes found on the X and Y chromosomes are 
not the same. 


Section Summary 


Prokaryotes have a single loop chromosome, whereas eukaryotes have 
multiple, linear chromosomes surrounded by a nuclear membrane. Human 
somatic cells have 46 chromosomes consisting of two sets of 22 
homologous chromosomes and a pair of nonhomologous sex chromosomes. 
This is the 2n, or diploid, state. Human gametes have 23 chromosomes or 
one complete set of chromosomes. This is the n, or haploid, state. Genes are 
segments of DNA that code for a specific protein or RNA molecule. An 
organism’s traits are determined in large part by the genes inherited from 
each parent, but also by the environment that they experience. Genes are 
expressed as characteristics of the organism and each characteristic may 
have different variants called traits that are caused by differences in the 
DNA sequence for a gene. 


Glossary 
diploid 
describes a cell, nucleus, or organism containing two sets of 


chromosomes (2n) 


gamete 
a haploid reproductive cell or sex cell (sperm or egg) 


gene 


the physical and functional unit of heredity; a sequence of DNA that 
codes for a specific peptide or RNA molecule 


genome 
the entire genetic complement (DNA) of an organism 


haploid 
describes a cell, nucleus, or organism containing one set of 
chromosomes (n) 


homologous chromosomes 
chromosomes of the same length with genes in the same location; 
diploid organisms have pairs of homologous chromosomes, and the 
members of each pair come from different parents 


locus 
the position of a gene on a chromosome 


How Genes Are Regulated EnBio 
By the end of this section, you will be able to: 


e Discuss why every cell does not express all of its genes 

e Describe how prokaryotic gene expression occurs at the transcriptional 
level 

e Understand that eukaryotic gene expression occurs at the epigenetic, 
transcriptional, post-transcriptional, translational, and post- 
translational levels 


For a cell to function properly, necessary proteins must be synthesized at 
the proper time. All organisms and cells control or regulate the transcription 
and translation of their DNA into protein. The process of turning on a gene 
to produce RNA and protein is called gene expression. Whether in a simple 
unicellular organism or in a complex multicellular organism, each cell 
controls when and how its genes are expressed. For this to occur, there must 
be a mechanism to control when a gene is expressed to make RNA and 
protein, how much of the protein is made, and when it is time to stop 
making that protein because it is no longer needed. 


Cells in multicellular organisms are specialized; cells in different tissues 
look very different and perform different functions. For example, a muscle 
cell is very different from a liver cell, which is very different from a skin 
cell. These differences are a consequence of the expression of different sets 
of genes in each of these cells. All cells have certain basic functions they 
must perform for themselves, such as converting the energy in sugar 
molecules into energy in ATP. Each cell also has many genes that are not 
expressed, and expresses many that are not expressed by other cells, such 
that it can carry out its specialized functions. In addition, cells will turn on 
or off certain genes at different times in response to changes in the 
environment or at different times during the development of the organism. 
Unicellular organisms, both eukaryotic and prokaryotic, also turn on and off 
genes in response to the demands of their environment so that they can 
respond to special conditions. 


The control of gene expression is extremely complex. Malfunctions in this 
process are detrimental to the cell and can lead to the development of many 
diseases, including cancer. 


Prokaryotic versus Eukaryotic Gene Expression 


To understand how gene expression is regulated, we must first understand 
how a gene becomes a functional protein in a cell. The process occurs in 
both prokaryotic and eukaryotic cells, just in slightly different fashions. 


Because prokaryotic organisms lack a cell nucleus, the processes of 
transcription and translation occur almost simultaneously. When the protein 
is no longer needed, transcription stops. As a result, the primary method to 
control what type and how much protein is expressed in a prokaryotic cell is 
through the regulation of DNA transcription into RNA. All the subsequent 
steps happen automatically. When more protein is required, more 
transcription occurs. Therefore, in prokaryotic cells, the control of gene 
expression is almost entirely at the transcriptional level. 


The first example of such control was discovered using E. coli in the 1950s 
and 1960s by French researchers and is called the lac operon. The lac 
operon is a stretch of DNA with three adjacent genes that code for proteins 
that participate in the absorption and metabolism of lactose, a food source 
for E. coli. When lactose is not present in the bacterium’s environment, the 
lac genes are transcribed in small amounts. When lactose is present, the 
genes are transcribed and the bacterium is able to use the lactose as a food 
source. 


Eukaryotic cells, in contrast, have intracellular organelles and are much 
more complex. Recall that in eukaryotic cells, the DNA is contained inside 
the cell’s nucleus and it is transcribed into mRNA there. The newly 
synthesized mRNA is then transported out of the nucleus into the 
cytoplasm, where ribosomes translate the mRNA into protein. The 
processes of transcription and translation are physically separated by the 
nuclear membrane; transcription occurs only within the nucleus, and 
translation only occurs outside the nucleus in the cytoplasm. The regulation 
of gene expression can occur at all stages of the process ({link]). Regulation 
may occur when the DNA is uncoiled and loosened from nucleosomes to 
bind transcription factors (epigenetic level), when the RNA is transcribed 
(transcriptional level), when RNA is processed and exported to the 
cytoplasm after it is transcribed (post-transcriptional level), when the 


RNA is translated into protein (translational level), or after the protein has 
been made (post-translational level). 


Transcription 


5\ RNA Nontemplate strand 
4, 
act 
ATGCCECKAGY ‘ 
(@) " 
C 3 
TACGCCCTTAGAC VU RE EEN Ue ATCCTCCAT 
3 a4 ch S' 


ETSCGTGAGTA 
DNA RNA polymerase Template strand 


RNA processing 
primary RNA transcript 


spliced RNA 


Translation 


polypeptide chain 


Ribosome 


Eukaryotic gene expression is 
regulated during transcription and 
RNA processing, which take place 

in the nucleus, as well as during 
protein translation, which takes 
place in the cytoplasm. Further 


regulation may occur through 
post-translational modifications of 
proteins. 


The differences in the regulation of gene expression between prokaryotes 
and eukaryotes are summarized in [link]. 


Differences in the Regulation of Gene Expression of Prokaryotic 
and Eukaryotic Organisms 


Prokaryotic 
organisms Eukaryotic organisms 
Lack nucleus Contain nucleus 

e RNA transcription occurs prior to 
RNA transcription protein translation, and it takes place in 
and protein the nucleus. RNA translation to protein 
translation occur occurs in the cytoplasm. 
almost e RNA post-processing includes addition 
simultaneously of a 5' cap, poly-A tail, and excision of 

introns and splicing of exons. 

Gene expression is Gene expression is regulated at many levels 
regulated primarily (epigenetic, transcriptional, post- 
at the transcriptional, translational, and post- 


transcriptional level translational) 


Section Summary 


While all somatic cells within an organism contain the same DNA, not all 
cells within that organism express the same proteins. Prokaryotic organisms 
express the entire DNA they encode in every cell, but not necessarily all at 
the same time. Proteins are expressed only when they are needed. 
Eukaryotic organisms express a subset of the DNA that is encoded in any 
given cell. In each cell type, the type and amount of protein is regulated by 
controlling gene expression. To express a protein, the DNA is first 
transcribed into RNA, which is then translated into proteins. In prokaryotic 
cells, these processes occur almost simultaneously. In eukaryotic cells, 
transcription occurs in the nucleus and is separate from the translation that 
occurs in the cytoplasm. Gene expression in prokaryotes is regulated only at 
the transcriptional level, whereas in eukaryotic cells, gene expression is 
regulated at the epigenetic, transcriptional, post-transcriptional, 
translational, and post-translational levels. 


Glossary 


alternative RNA splicing 
a post-transcriptional gene regulation mechanism in eukaryotes in 
which multiple protein products are produced by a single gene through 
alternative splicing combinations of the RNA transcript 


epigenetic 
describing non-genetic regulatory factors, such as changes in 
modifications to histone proteins and DNA that control accessibility to 
genes in chromosomes 


gene expression 
processes that control whether a gene is expressed 


post-transcriptional 
control of gene expression after the RNA molecule has been created 
but before it is translated into protein 


post-translational 


control of gene expression after a protein has been created 


The Human Population EnBio 
By the end of this section, you will be able to: 


e Discuss how human population growth can be exponential 

e Explain how humans have expanded the carrying capacity of their 
habitat 

¢ Relate population growth and age structure to the level of economic 
development in different countries 

e Discuss the long-term implications of unchecked human population 
growth 


Concepts of animal population dynamics can be applied to human 
population growth. Humans are not unique in their ability to alter their 
environment. For example, beaver dams alter the stream environment where 
they are built. Humans, however, have the ability to alter their environment 
to increase its carrying capacity, sometimes to the detriment of other 
species. Earth’s human population and their use of resources are growing 
rapidly, to the extent that some worry about the ability of Earth’s 
environment to sustain its human population. Long-term exponential 
growth carries with it the potential risks of famine, disease, and large-scale 
death, as well as social consequences of crowding such as increased crime. 


Human technology and particularly our harnessing of the energy contained 
in fossil fuels have caused unprecedented changes to Earth’s environment, 
altering ecosystems to the point where some may be in danger of collapse. 
Changes on a global scale including depletion of the ozone layer, 
desertification and topsoil loss, and global climate change are caused by 
human activities. 


The world’s human population is presently growing exponentially ([Link]). 


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Human population growth since 
1000 AD is exponential. 


A consequence of exponential growth rate is that the time that it takes to 
add a particular number of humans to the population is becoming shorter. 
[link] shows that 123 years were necessary to add 1 billion humans between 
1804 and 1930, but it only took 24 years to add the two billion people 
between 1975 and 1999. This acceleration in growth rate will likely begin 
to decrease in the coming decades. Despite this, the population will 
continue to increase and the threat of overpopulation remains, particularly 
because the damage caused to ecosystems and biodiversity is lowering the 
human carrying capacity of the planet. 


Time between Billions in World Population Growth 


1 billion: 1800 
2 billion: 1930 
3 billion: 1960 
4 billion: 1975 
5 billion: 1987 
6 billion: 1999 
7 billion: 2012 
8 billion: 2028 
9 billion: 2054 


20 40 60 80 100 120 140 
Years 


Source: Population Reference Bureau 


The time between the addition of each billion 
human beings to Earth decreases over time. 
(credit: modification of work by Ryan T. Cragun) 


Note: 
Concept in Action 


OR [=] 


2 


Click through this interactive view of how human populations have 
changed over time. 


Overcoming Density-Dependent Regulation 


Humans are unique in their ability to alter their environment in myriad 
ways. This ability is responsible for human population growth because it 
resets the carrying capacity and overcomes density-dependent growth 
regulation. Much of this ability is related to human intelligence, society, and 
communication. Humans construct shelters to protect themselves from the 
elements and have developed agriculture and domesticated animals to 
increase their food supplies. In addition, humans use language to 
communicate this technology to new generations, allowing them to improve 
upon previous accomplishments. 


Other factors in human population growth are migration and public health. 
Humans originated in Africa, but we have since migrated to nearly all 
inhabitable land on Earth, thus, increasing the area that we have colonized. 
Public health, sanitation, and the use of antibiotics and vaccines have 
decreased the ability of infectious disease to limit human population growth 
in developed countries. In the past, diseases such as the bubonic plaque of 
the fourteenth century killed between 30 and 60 percent of Europe’s 
population and reduced the overall world population by as many as one 
hundred million people. Infectious disease continues to have an impact on 
human population growth. For example, life expectancy in sub-Saharan 
Africa, which was increasing from 1950 to 1990, began to decline after 
1985 largely as a result of HIV/AIDS mortality. The reduction in life 
expectancy caused by HIV/AIDS was estimated to be 7 years for 2005. 
[footnote | 

Danny Dorling, Mary Shaw, and George Davey Smith, “Global Inequality 
of Life Expectancy due to AIDS,” BMJ 332, no. 7542 (March 2006): 662- 
664, doi: 10.1136/bmj.332.7542.662. 


Declining life expectancy is an indicator of higher mortality rates and leads 
to lower birth rates. 


The fundamental cause of the acceleration of growth rate for humans in the 
past 200 years has been the reduced death rate due to a development of the 
technological advances of the industrial age, urbanization that supported 
those technologies, and especially the exploitation of the energy in fossil 
fuels. Fossil fuels are responsible for dramatically increasing the resources 


available for human population growth through agriculture (mechanization, 
pesticides, and fertilizers) and harvesting wild populations. 


Age Structure, Population Growth, and Economic 
Development 


The age structure of a population is an important factor in population 
dynamics. Age structure is the proportion of a population in different age 
classes. Models that incorporate age structure allow better prediction of 
population growth, plus the ability to associate this growth with the level of 
economic development in a region. Countries with rapid growth have a 
pyramidal shape in their age structure diagrams, showing a preponderance 
of younger individuals, many of whom are of reproductive age ([link]). This 
pattern is most often observed in underdeveloped countries where 
individuals do not live to old age because of less-than-optimal living 
conditions, and there is a high birth rate. Age structures of areas with slow 
growth, including developed countries such as the United States, still have a 
pyramidal structure, but with many fewer young and reproductive-aged 
individuals and a greater proportion of older individuals. Other developed 
countries, such as Italy, have zero population growth. The age structure of 
these populations is more conical, with an even greater percentage of 
middle-aged and older individuals. The actual growth rates in different 
countries are shown in [link], with the highest rates tending to be in the less 
economically developed countries of Africa and Asia. 


Note: 
Art Connection 


Age Structure Diagrams 


Stage 1: Rapid growth Stage 2: Slow growth Stage 3: Stable Stage 4: ? 


Typical age structure diagrams are shown. The rapid 
growth diagram narrows to a point, indicating that the 
number of individuals decreases rapidly with age. In the 
slow growth model, the number of individuals decreases 
steadily with age. Stable population diagrams are rounded 
on the top, showing that the number of individuals per age 
group decreases gradually, and then increases for the older 
part of the population. 


Age structure diagrams for rapidly growing, slow growing, and stable 
populations are shown in stages 1 through 3. What type of population 
change do you think stage 4 represents? 


Percent Growth in Population 


M-0% M0%-1% M1% Hx 


The percent growth rate of population in different countries is 
shown. Notice that the highest growth is occurring in less 
economically developed countries in Africa and Asia. 


Long-Term Consequences of Exponential Human Population 
Growth 


Many dire predictions have been made about the world’s population leading 
to a major crisis called the “population explosion.” In the 1968 book The 
Population Bomb, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed 
all of humanity is over. In the 1970s hundreds of millions of people will 
Starve to death in spite of any crash programs embarked upon now. At this 
late date nothing can prevent a substantial increase in the world death 

rate,” footnote] While many critics view this statement as an exaggeration, the 
laws of exponential population growth are still in effect, and unchecked 
human population growth cannot continue indefinitely. 

Paul R. Erlich, prologue to The Population Bomb, (1968; repr., New York: 
Ballantine, 1970). 


The United Nations estimates the future world population size could vary 
from 6 billion (a decrease) to 16 billion people by the year 2100. There is 
no way to know whether human population growth will moderate to the 
point where the crisis described by Dr. Ehrlich will be averted. 


Another consequence of population growth is the change and degradation 
of the natural environment. Many countries have attempted to reduce the 
human impact on climate change by limiting their emission of greenhouse 
gases. However, a global climate change treaty remains elusive, and many 
underdeveloped countries trying to improve their economic condition may 
be less likely to agree with such provisions without compensation if it 
means slowing their economic development. Furthermore, the role of 
human activity in causing climate change has become a hotly debated 
socio-political issue in some developed countries, including the United 
States. Thus, we enter the future with considerable uncertainty about our 
ability to curb human population growth and protect our environment to 
maintain the carrying capacity for the human species. 


Note: 
Concept in Action 


= 
mess" OPenstax COLLEGE 
A 


Visit this website and select “Launch the movie” for an animation 
discussing the global impacts of human population growth. 


Section Summary 


Earth’s human population is growing exponentially. Humans have increased 
their carrying capacity through technology, urbanization, and harnessing the 
energy of fossil fuels. The age structure of a population allows us to predict 
population growth. Unchecked human population growth could have dire 
long-term effects on human welfare and Earth’s ecosystems. 


Glossary 


age structure 
the distribution of the proportion of population members in each age 
class 


one-child policy 
a policy in China to limit population growth by limiting urban couples 
to have only one child or face a penalty of a fine 


Importance of Biodiversity EnBio 
By the end of this section, you will be able to: 


e Describe biodiversity as the equilibrium of naturally fluctuating rates of extinction and speciation 
e Identify benefits of biodiversity to humans 


This tropical lowland rainforest in 
Madagascar is an example of a 
high biodiversity habitat. This 
particular location is protected 

within a national forest, yet only 
10 percent of the original coastal 
lowland forest remains, and 
research suggests half the original 
biodiversity has been lost. (credit: 
Frank Vassen) 


Biodiversity is a broad term for biological variety, and it can be measured at a number of organizational levels. 
Traditionally, ecologists have measured biodiversity by taking into account both the number of species and the 
number of individuals in each of those species. However, biologists are using measures of biodiversity at several 
levels of biological organization (including genes, populations, and ecosystems) to help focus efforts to preserve 
the biologically and technologically important elements of biodiversity. 


Biologists recognize that human populations are embedded in ecosystems and are dependent on them, just as is 
every other species on the planet. Agriculture began after early hunter-gatherer societies first settled in one place 
and heavily modified their immediate environment: the ecosystem in which they existed. This cultural transition 
has made it difficult for humans to recognize their dependence on living things other than crops and domesticated 
animals on the planet. Today our technology smoothes out the extremes of existence and allows many of us to live 
longer, more comfortable lives, but ultimately the human species cannot exist without its surrounding ecosystems. 
Our ecosystems provide our food. This includes living plants that grow in soil ecosystems and the animals that eat 
these plants (or other animals) as well as photosynthetic organisms in the oceans and the other organisms that eat 
them. Our ecosystems have provided and will provide many of the medications that maintain our health, which are 
commonly made from compounds found in living organisms. Ecosystems provide our clean water, which is held in 
lake and river ecosystems or passes through terrestrial ecosystems on its way into groundwater. 


Types of Biodiversity 


A common meaning of biodiversity is simply the number of species in a location or on Earth; for example, the 
American Ornithologists’ Union lists 2078 species of birds in North and Central America. This is one measure of 
the bird biodiversity on the continent. More sophisticated measures of diversity take into account the relative 
abundances of species. For example, a forest with 10 equally common species of trees is more diverse than a forest 
that has 10 species of trees wherein just one of those species makes up 95 percent of the trees rather than them 


being equally distributed. Biologists have also identified alternate measures of biodiversity, some of which are 
important in planning how to preserve biodiversity. 


Genetic and Chemical Biodiversity 


Genetic diversity is one alternate concept of biodiversity. Genetic diversity (or variation) is the raw material for 
adaptation in a species. A species’ future potential for adaptation depends on the genetic diversity held in the 
genomes of the individuals in populations that make up the species. 


Most genes code for proteins, which in turn carry out the metabolic processes that keep organisms alive and 
reproducing. Genetic diversity can also be conceived of as chemical diversity in that species with different genetic 
makeups produce different assortments of chemicals in their cells (proteins as well as the products and byproducts 
of metabolism). This chemical diversity is important for humans because of the potential uses for these chemicals, 
such as medications. For example, the drug eptifibatide is derived from rattlesnake venom and is used to prevent 
heart attacks in individuals with certain heart conditions. 


At present, it is far cheaper to discover compounds made by an organism than to imagine them and then synthesize 
them in a laboratory. Chemical diversity is one way to measure diversity that is important to human health and 
welfare. Through selective breeding, humans have domesticated animals, plants, and fungi, but even this diversity 
is suffering losses because of market forces and increasing globalism in human agriculture and migration. For 
example, international seed companies produce only a very few varieties of a given crop and provide incentives 
around the world for farmers to buy these few varieties while abandoning their traditional varieties, which are far 
more diverse. The human population depends on crop diversity directly as a stable food source and its decline is 
troubling to biologists and agricultural scientists. 


Ecosystems Diversity 


It is also useful to define ecosystem diversity: the number of different ecosystems on Earth or in a geographical 
area. Whole ecosystems can disappear even if some of the species might survive by adapting to other ecosystems. 
The loss of an ecosystem means the loss of the interactions between species, the loss of unique features of 
coadaptation, and the loss of biological productivity that an ecosystem is able to create. An example of a largely 
extinct ecosystem in North America is the prairie ecosystem ([link]). Prairies once spanned central North America 
from the boreal forest in northern Canada down into Mexico. They are now all but gone, replaced by crop fields, 
pasture lands, and suburban sprawl. Many of the species survive, but the hugely productive ecosystem that was 
responsible for creating our most productive agricultural soils is now gone. As a consequence, their soils are now 
being depleted unless they are maintained artificially at greater expense. The decline in soil productivity occurs 
because the interactions in the original ecosystem have been lost; this was a far more important loss than the 
relatively few species that were driven extinct when the prairie ecosystem was destroyed. 


The variety of ecosystems on Earth—from coral reef to 
prairie—enables a great diversity of species to exist. 
(credit “coral reef”: modification of work by Jim 


Maragos, USFWS; credit: “prairie”: modification of 
work by Jim Minnerath, USFWS) 


Current Species Diversity 


Despite considerable effort, knowledge of the species that inhabit the planet is limited. A recent estimate suggests 
that the eukaryote species for which science has names, about 1.5 million species, account for less than 20 percent 
of the total number of eukaryote species present on the planet (8.7 million species, by one estimate). Estimates of 
numbers of prokaryotic species are largely guesses, but biologists agree that science has only just begun to catalog 
their diversity. Even with what is known, there is no centralized repository of names or samples of the described 
species; therefore, there is no way to be sure that the 1.5 million descriptions is an accurate number. It is a best 
guess based on the opinions of experts on different taxonomic groups. Given that Earth is losing species at an 
accelerating pace, science knows little about what is being lost. [link] presents recent estimates of biodiversity in 
different groups. 


Estimated Numbers of Described and Predicted species 


Source: Groombridge 


Source: Mora et al 2011 Source: Chapman 2009 and Jenkins 2002 
Described Predicted Described Predicted Described Predicted 
Animals 1,124,516 9,920,000 1,424,153 6,836,330 1,225,500 10,820,000 
Photosynthetic | 17 g99 34,900 25,044 200,500 = = 
protists 
Fungi 44,368 616,320 98,998 1,500,000 72,000 1,500,000 
Plants 224,244 314,600 310,129 390,800 270,000 320,000 
Non- 
photosynthetic 16,236 72,800 28,871 1,000,000 80,000 600,000 
protists 
Prokaryotes — — 10,307 1,000,000 10,175 — 
Total 1,438,769 10,960,000 1,897,502 10,897,630 1,657,675 13,240,000 


This table shows the estimated number of species by taxonomic group—including both described (named and 
studied) and predicted (yet to be named) species. 


There are various initiatives to catalog described species in accessible and more organized ways, and the internet is 
facilitating that effort. Nevertheless, at the current rate of species description, which according to the State of 
Observed Species!!22™ote] reports is 17,000—-20,000 new species a year, it would take close to 500 years to describe 
all of the species currently in existence. The task, however, is becoming increasingly impossible over time as 
extinction removes species from Earth faster than they can be described. 


International Institute for Species Exploration (IISE), 2011 State of Observed Species (SOS). Tempe, AZ: IISE, 
2011. Accessed May, 20, 2012. http://species.asu.edu/SOS. 


Patterns of Biodiversity 


Biodiversity is not evenly distributed on the planet. Lake Victoria contained almost 500 species of cichlids (only 
one family of fishes present in the lake) before the introduction of an exotic species in the 1980s and 1990s caused 
a mass extinction. All of these species were found only in Lake Victoria, which is to say they were endemic. 
Endemic species are found in only one location. For example, the blue jay is endemic to North America, while the 
Barton Springs salamander is endemic to the mouth of one spring in Austin, Texas. Endemics with highly 
restricted distributions, like the Barton Springs salamander, are particularly vulnerable to extinction. Higher 
taxonomic levels, such as genera and families, can also be endemic. 


Lake Huron contains about 79 species of fish, all of which are found in many other lakes in North America. What 
accounts for the difference in diversity between Lake Victoria and Lake Huron? Lake Victoria is a tropical lake, 
while Lake Huron is a temperate lake. Lake Huron in its present form is only about 7,000 years old, while Lake 
Victoria in its present form is about 15,000 years old. These two factors, latitude and age, are two of several 
hypotheses biogeographers have suggested to explain biodiversity patterns on Earth. 


One of the oldest observed patterns in ecology is that biodiversity in almost every taxonomic group of organism 
increases as latitude declines. In other words, biodiversity increases closer to the equator ((link]). 


Number of species 
C0 mi m@ 2-3 mm 4-6 @ 7-10 @ 11-15 


16-20 BW 21-30 @ 31-40 @ 41-60 @® 61-144 


This map illustrates the number of amphibian species 
across the globe and shows the trend toward higher 
biodiversity at lower latitudes. A similar pattern is 

observed for most taxonomic groups. 


It is not yet clear why biodiversity increases closer to the equator, but hypotheses include the greater age of the 
ecosystems in the tropics versus temperate regions, which were largely devoid of life or drastically impoverished 
during the last ice age. The greater age provides more time for speciation. Another possible explanation is the 
greater energy the tropics receive from the sun versus the lesser energy input in temperate and polar regions. But 
scientists have not been able to explain how greater energy input could translate into more species. The complexity 
of tropical ecosystems may promote speciation by increasing the habitat heterogeneity, or number of ecological 
niches, in the tropics relative to higher latitudes. The greater heterogeneity provides more opportunities for 
coevolution, specialization, and perhaps greater selection pressures leading to population differentiation. However, 
this hypothesis suffers from some circularity—ecosystems with more species encourage speciation, but how did 
they get more species to begin with? The tropics have been perceived as being more stable than temperate regions, 
which have a pronounced climate and day-length seasonality. The tropics have their own forms of seasonality, such 


as rainfall, but they are generally assumed to be more stable environments and this stability might promote 
speciation. 


Regardless of the mechanisms, it is certainly true that biodiversity is greatest in the tropics. The number of 
endemic species is higher in the tropics. The tropics also contain more biodiversity hotspots. At the same time, our 
knowledge of the species living in the tropics is lowest and because of recent, heavy human activity the potential 
for biodiversity loss is greatest. 


Importance of Biodiversity 


Loss of biodiversity eventually threatens other species we do not impact directly because of their 
interconnectedness; as species disappear from an ecosystem other species are threatened by the changes in 
available resources. Biodiversity is important to the survival and welfare of human populations because it has 
impacts on our health and our ability to feed ourselves through agriculture and harvesting populations of wild 
animals. 


Human Health 


Many medications are derived from natural chemicals made by a diverse group of organisms. For example, many 
plants produce secondary plant compounds, which are toxins used to protect the plant from insects and other 
animals that eat them. Some of these secondary plant compounds also work as human medicines. Contemporary 
societies that live close to the land often have a broad knowledge of the medicinal uses of plants growing in their 
area. For centuries in Europe, older knowledge about the medical uses of plants was compiled in herbals—books 
that identified the plants and their uses. Humans are not the only animals to use plants for medicinal reasons. The 
other great apes, orangutans, chimpanzees, bonobos, and gorillas have all been observed self-medicating with 
plants. 


Modern pharmaceutical science also recognizes the importance of these plant compounds. Examples of significant 
medicines derived from plant compounds include aspirin, codeine, digoxin, atropine, and vincristine ({link]). Many 
medications were once derived from plant extracts but are now synthesized. It is estimated that, at one time, 25 
percent of modern drugs contained at least one plant extract. That number has probably decreased to about 10 
percent as natural plant ingredients are replaced by synthetic versions of the plant compounds. Antibiotics, which 
are responsible for extraordinary improvements in health and lifespans in developed countries, are compounds 
largely derived from fungi and bacteria. 


Catharanthus roseus, the 
Madagascar periwinkle, has 
various medicinal properties. 

Among other uses, it is a 
source of vincristine, a drug 

used in the treatment of 


lymphomas. (credit: Forest 
and Kim Starr) 


In recent years, animal venoms and poisons have excited intense research for their medicinal potential. By 2007, 
the FDA had approved five drugs based on animal toxins to treat diseases such as hypertension, chronic pain, and 
diabetes. Another five drugs are undergoing clinical trials and at least six drugs are being used in other countries. 
Other toxins under investigation come from mammals, snakes, lizards, various amphibians, fish, snails, octopuses, 
and scorpions. 


Aside from representing billions of dollars in profits, these medications improve people’s lives. Pharmaceutical 
companies are actively looking for new natural compounds that can function as medicines. It is estimated that one 
third of pharmaceutical research and development is spent on natural compounds and that about 35 percent of new 
drugs brought to market between 1981 and 2002 were from natural compounds. 


Finally, it has been argued that humans benefit psychologically from living in a biodiverse world. The chief 
proponent of this idea is entomologist E. O. Wilson. He argues that human evolutionary history has adapted us to 
living in a natural environment and that built environments generate stresses that affect human health and well- 
being. There is considerable research into the psychologically regenerative benefits of natural landscapes that 
suggest the hypothesis may hold some truth. 


Agricultural 


Since the beginning of human agriculture more than 10,000 years ago, human groups have been breeding and 
selecting crop varieties. This crop diversity matched the cultural diversity of highly subdivided populations of 
humans. For example, potatoes were domesticated beginning around 7,000 years ago in the central Andes of Peru 
and Bolivia. The people in this region traditionally lived in relatively isolated settlements separated by mountains. 
The potatoes grown in that region belong to seven species and the number of varieties likely is in the thousands. 
Each variety has been bred to thrive at particular elevations and soil and climate conditions. The diversity is driven 
by the diverse demands of the dramatic elevation changes, the limited movement of people, and the demands 
created by crop rotation for different varieties that will do well in different fields. 


Potatoes are only one example of agricultural diversity. Every plant, animal, and fungus that has been cultivated by 
humans has been bred from original wild ancestor species into diverse varieties arising from the demands for food 
value, adaptation to growing conditions, and resistance to pests. The potato demonstrates a well-known example of 
the risks of low crop diversity: during the tragic Irish potato famine (1845-1852 AD), the single potato variety 
grown in Ireland became susceptible to a potato blight—wiping out the crop. The loss of the crop led to famine, 
death, and mass emigration. Resistance to disease is a chief benefit to maintaining crop biodiversity and lack of 
diversity in contemporary crop species carries similar risks. Seed companies, which are the source of most crop 
varieties in developed countries, must continually breed new varieties to keep up with evolving pest organisms. 
These same seed companies, however, have participated in the decline of the number of varieties available as they 
focus on selling fewer varieties in more areas of the world replacing traditional local varieties. 


The ability to create new crop varieties relies on the diversity of varieties available and the availability of wild 
forms related to the crop plant. These wild forms are often the source of new gene variants that can be bred with 
existing varieties to create varieties with new attributes. Loss of wild species related to a crop will mean the loss of 
potential in crop improvement. Maintaining the genetic diversity of wild species related to domesticated species 
ensures our continued supply of food. 


Since the 1920s, government agriculture departments have maintained seed banks of crop varieties as a way to 
maintain crop diversity. This system has flaws because over time seed varieties are lost through accidents and there 
is no way to replace them. In 2008, the Svalbard Global seed Vault, located on Spitsbergen island, Norway, ([Llink]) 
began storing seeds from around the world as a backup system to the regional seed banks. If a regional seed bank 
stores varieties in Svalbard, losses can be replaced from Svalbard should something happen to the regional seeds. 


The Svalbard seed vault is deep into the rock of the arctic island. Conditions within the vault are maintained at 
ideal temperature and humidity for seed survival, but the deep underground location of the vault in the arctic 
means that failure of the vault’s systems will not compromise the climatic conditions inside the vault. 


Note: 
Art Connection 


The Svalbard Global Seed 
Vault is a storage facility for 
seeds of Earth’s diverse 
crops. (credit: Mari Tefre, 
Svalbard Global Seed Vault) 


The Svalbard seed vault is located on Spitsbergen island in Norway, which has an arctic climate. Why might an 
arctic climate be good for seed storage? 


Although crops are largely under our control, our ability to grow them is dependent on the biodiversity of the 
ecosystems in which they are grown. That biodiversity creates the conditions under which crops are able to grow 
through what are known as ecosystem services—valuable conditions or processes that are carried out by an 
ecosystem. Crops are not grown, for the most part, in built environments. They are grown in soil. Although some 
agricultural soils are rendered sterile using controversial pesticide treatments, most contain a huge diversity of 
organisms that maintain nutrient cycles—breaking down organic matter into nutrient compounds that crops need 
for growth. These organisms also maintain soil texture that affects water and oxygen dynamics in the soil that are 
necessary for plant growth. Replacing the work of these organisms in forming arable soil is not practically 
possible. These kinds of processes are called ecosystem services. They occur within ecosystems, such as soil 
ecosystems, as a result of the diverse metabolic activities of the organisms living there, but they provide benefits to 
human food production, drinking water availability, and breathable air. 


Other key ecosystem services related to food production are plant pollination and crop pest control. It is estimated 
that honeybee pollination within the United States brings in $1.6 billion per year; other pollinators contribute up to 
$6.7 billion. Over 150 crops in the United States require pollination to produce. Many honeybee populations are 
managed by beekeepers who rent out their hives’ services to farmers. Honeybee populations in North America 
have been suffering large losses caused by a syndrome known as colony collapse disorder, a new phenomenon 
with an unclear cause. Other pollinators include a diverse array of other bee species and various insects and birds. 
Loss of these species would make growing crops requiring pollination impossible, increasing dependence on other 
crops. 


Finally, humans compete for their food with crop pests, most of which are insects. Pesticides control these 
competitors, but these are costly and lose their effectiveness over time as pest populations adapt. They also lead to 
collateral damage by killing non-pest species as well as beneficial insects like honeybees, and risking the health of 
agricultural workers and consumers. Moreover, these pesticides may migrate from the fields where they are 
applied and do damage to other ecosystems like streams, lakes, and even the ocean. Ecologists believe that the 


bulk of the work in removing pests is actually done by predators and parasites of those pests, but the impact has 
not been well studied. A review found that in 74 percent of studies that looked for an effect of landscape 
complexity (forests and fallow fields near to crop fields) on natural enemies of pests, the greater the complexity, 
the greater the effect of pest-suppressing organisms. Another experimental study found that introducing multiple 
enemies of pea aphids (an important alfalfa pest) increased the yield of alfalfa significantly. This study shows that 
a diversity of pests is more effective at control than one single pest. Loss of diversity in pest enemies will 
inevitably make it more difficult and costly to grow food. The world’s growing human population faces significant 
challenges in the increasing costs and other difficulties associated with producing food. 


Wild Food Sources 


In addition to growing crops and raising food animals, humans obtain food resources from wild populations, 
primarily wild fish populations. For about one billion people, aquatic resources provide the main source of animal 
protein. But since 1990, production from global fisheries has declined. Despite considerable effort, few fisheries 
on Earth are managed sustainability. 


Fishery extinctions rarely lead to complete extinction of the harvested species, but rather to a radical restructuring 
of the marine ecosystem in which a dominant species is so over-harvested that it becomes a minor player, 
ecologically. In addition to humans losing the food source, these alterations affect many other species in ways that 
are difficult or impossible to predict. The collapse of fisheries has dramatic and long-lasting effects on local human 
populations that work in the fishery. In addition, the loss of an inexpensive protein source to populations that 
cannot afford to replace it will increase the cost of living and limit societies in other ways. In general, the fish 
taken from fisheries have shifted to smaller species and the larger species are overfished. The ultimate outcome 
could clearly be the loss of aquatic systems as food sources. 


Note: 
Concept in Action 


= openstax couse 


Visit this website to view a brief video discussing a study of declining fisheries. 


Section Summary 


Biodiversity exists at multiple levels of organization, and is measured in different ways depending on the goals of 
those taking the measurements. These include numbers of species, genetic diversity, chemical diversity, and 
ecosystem diversity. The number of described species is estimated to be 1.5 million with about 17,000 new species 
being described each year. Estimates for the total number of eukaryotic species on Earth vary but are on the order 
of 10 million. Biodiversity is negatively correlated with latitude for most taxa, meaning that biodiversity is higher 
in the tropics. The mechanism for this pattern is not known with certainty, but several plausible hypotheses have 
been advanced. 


Humans use many compounds that were first discovered or derived from living organisms as medicines: secondary 
plant compounds, animal toxins, and antibiotics produced by bacteria and fungi. More medicines are expected to 
be discovered in nature. Loss of biodiversity will impact the number of pharmaceuticals available to humans. 
Biodiversity may provide important psychological benefits to humans. 


Crop diversity is a requirement for food security, and it is being lost. The loss of wild relatives to crops also 
threatens breeders’ abilities to create new varieties. Ecosystems provide ecosystem services that support human 
agriculture: pollination, nutrient cycling, pest control, and soil development and maintenance. Loss of biodiversity 
threatens these ecosystem services and risks making food production more expensive or impossible. Wild food 
sources are mainly aquatic, but few are being managed for sustainability. Fisheries’ ability to provide protein to 
human populations is threatened when extinction occurs. 


Glossary 


biodiversity 
the variety of a biological system, typically conceived as the number of species, but also applying to genes, 
biochemistry, and ecosystems 


chemical diversity 
the variety of metabolic compounds in an ecosystem 


ecosystem diversity 
the variety of ecosystems 


endemic species 
a species native to one place 


extinction 
the disappearance of a species from Earth; local extinction is the disappearance of a species from a region 


genetic diversity 
the variety of genes and alleles in a species or other taxonomic group or ecosystem; the term can refer to 
allelic diversity or genome-wide diversity 


habitat heterogeneity 
the number of ecological niches 


secondary plant compound 
a compound produced as a byproduct of plant metabolic processes that is typically toxic, but is sequestered by 
the plant to defend against herbivores 


Introduction Biotechnology EnBio 
class="introduction" 


(a)A 
thermal 
cycler, such 
as the one 
shown here, 
is a basic 
tool used to 
study DNA 
in a process 
called the 
polymerase 
chain 
reaction 
(PCR). The 
polymerase 
enzyme 
most often 
used with 
PCR comes 
from a 
strain of 
bacteria that 
lives in (b) 
the hot 
springs of 
Yellowstone 
National 
Park. (credit 
a: 
modificatio 
n of work 
by Magnus 
Manske; 
credit b: 


modificatio 
n of work 
by Jon 
Sullivan) 


(a) 


The latter half of the twentieth century began with the discovery of the 
structure of DNA, then progressed to the development of the basic tools 
used to study and manipulate DNA. These advances, as well as advances in 
our understanding of and ability to manipulate cells, have led some to refer 
to the twenty-first century as the biotechnology century. The rate of 
discovery and of the development of new applications in medicine, 
agriculture, and energy is expected to accelerate, bringing huge benefits to 
humankind and perhaps also significant risks. Many of these developments 
are expected to raise significant ethical and social questions that human 
societies have not yet had to consider. 


Introduction Conservation & Biodiversity EnBio 
class="introduction" 


Habitat 
destruction 
through 
deforestation 
, especially 
of tropical 
rainforests as 
seen in this 
satellite view 
of Amazon 
rainforests in 
Brazil, is a 
major cause 
of the current 
decline in 
biodiversity. 
(credit: 
modification 
of work by 
Jesse Allen 
and Robert 
Simmon, 
NASA Earth 
Observatory) 


Biologists estimate that species extinctions are currently 500—1000 times 
the rate seen previously in Earth’s history when there were no unusual 
geological or climatic events occurring. Biologists call the previous rate the 
“background” rate of extinction. The current high rates will cause a 
precipitous decline in the biodiversity (the diversity of species) of the planet 
in the next century or two. The losses will include many species we know 
today. Although it is sometimes difficult to predict which species will 
become extinct, many are listed as endangered (at great risk of extinction). 
However, the majority of extinctions will be of species that science has not 
yet even described. 


Most of these “invisible” species that will become extinct currently live in 
tropical rainforests like those of the Amazon basin. These rainforests are the 
most diverse ecosystems on the planet and are being destroyed rapidly by 
deforestation, which biologists believe is driving many rare species with 


limited distributions extinct. Between 1970 and 2011, almost 20 percent of 
the Amazon rainforest was lost. Rates are higher in other tropical 
rainforests. What we are likely to notice on a day-to-day basis as a result of 
biodiversity loss is that food will be more difficult to produce, clean water 
will be more difficult to find, and the rate of development of new medicines 
will become slower, as we depend upon other species for much of these 
services. This increased loss of biodiversity is almost entirely a result of 
human activities as we destroy species’ habitats, introduce disruptive 
species into ecosystems, hunt some species to extinction, continue to warm 
the planet with greenhouse gases, and influence nature in other ways. 
Slowing the loss of biodiversity is within our abilities if we make dramatic 
changes in our consumptive behavior and identify and protect the elements 
of our ecosystems that we depend on for our lives and welfare. 


Introduction Ecology EnBio 
class="introduction" 


Asian carp 
jump out of 
the water in 
response to 
electrofishing 
. The Asian 
carp in the 
inset 
photograph 
were 
harvested 
from the 
Little 
Calumet 
River in 
Illinois in 
May, 2010, 
using 
rotenone, a 
toxin often 
used as an 
insecticide, in 
an effort to 
learn more 
about the 
population of 
the species. 
(credit main 
image: 
modification 
of work by 
USGS; credit 
inset: 
modification 


of work by 

Lt. David 
French, 
USCG) 


Imagine sailing down a river in a small motorboat on a weekend afternoon; 
the water is smooth, and you are enjoying the sunshine and cool breeze 
when suddenly you are hit in the head by a 20-pound silver carp. This is a 
risk now on many rivers and canal systems in Illinois and Missouri because 
of the presence of Asian carp. 


This fish—actually a group of species including the silver, black, grass, and 
big head carp—has been farmed and eaten in China for over 1,000 years. It 
is one of the most important aquaculture food resources worldwide. In the 
United States, however, Asian carp is considered a dangerous invasive 
species that disrupts ecological community structure to the point of 
threatening native species. 


The effects of invasive species (such as the Asian carp, kudzu vine, 
predatory snakehead fish, and zebra mussel) are just one aspect of what 
ecologists study to understand how populations interact within ecological 


communities, and what impact natural and human-induced disturbances 
have on the characteristics of communities. 


Introduction Ecosystems & Biosphere EnBio 
class="introduction" 


The (a) Karner 
blue butterfly 
and (b) wild 
lupine live in 
oak-pine 
barren habitats 
in North 
America. 
(credit a: 
modification 
of work by 
John & Karen 
Hollingsworth 
, USFWS) 


Ecosystem ecology is an extension of organismal, population, and 
community ecology. The ecosystem comprises all the biotic components 
(living things) and abiotic components (non-living things) in a particular 
geographic area. Some of the abiotic components include air, water, soil, 
and climate. Ecosystem biologists study how nutrients and energy are 
stored and moved among organisms and the surrounding atmosphere, soil, 
and water. 


Wild lupine and Karner blue butterflies live in an oak-pine barren habitat in 
portions of Indiana, Michigan, Minnesota, Wisconsin, and New York 
({link]). This habitat is characterized by natural disturbance in the form of 
fire and nutrient-poor soils that are low in nitrogen—important factors in 
the distribution of the plants that live in this habitat. Researchers interested 
in ecosystem ecology study the importance of limited resources in this 
ecosystem and the movement of resources (such as nutrients) through the 
biotic and abiotic portions of the ecosystem. Researchers also examine how 
organisms have adapted to their ecosystem. 


Introduction Evolution & Its Processes EnBio 
class="introduction" 


The diversity 
of life on 
Earth is the 
result of 
evolution, a 
continuous 
process that 
is still 
occurring. 
(credit 
“wolf”: 
modification 
of work by 
Gary 
Kramer, 
USFWS; 
credit 
“coral”: 
modification 
of work by 
William 
Harrigan, 
NOAA; 
credit 
“river”: 
modification 
of work by 
Vojtéch 
Dostal; 
credit 
“protozoa”: 
modification 
of work by 
Sharon 


Franklin, 
Stephen 
Ausmus, 
USDA ARS; 
credit “fish” 
modification 
of work by 
Christian 
Mehl fiihrer; 
credit 
“mushroom” 
, “bee”: 
modification 
of work by 
Cory Zanker; 
credit “tree”: 
modification 
of work by 
Joseph 
Kranak) 


All species of living organisms—from the bacteria on our skin, to the trees 
in our yards, to the birds outside—evolved at some point from a different 
species. Although it may seem that living things today stay much the same 
from generation to generation, that is not the case: evolution is ongoing. 
Evolution is the process through which the characteristics of species change 
and through which new species arise. 


The theory of evolution is the unifying theory of biology, meaning it is the 
framework within which biologists ask questions about the living world. Its 
power is that it provides direction for predictions about living things that 
are borne out in experiment after experiment. The Ukrainian-born 
American geneticist Theodosius Dobzhansky famously wrote that “nothing 
makes sense in biology except in the light of evolution.”!{0™2e] He meant 
that the principle that all life has evolved and diversified from a common 
ancestor is the foundation from which we understand all other questions in 
biology. 

Theodosius Dobzhansky. “Biology, Molecular and Organismic.” American 
Zoologist 4, no. 4 (1964): 449. 


Introduction Molecular Biology EnBio 
class="introduction" 


Dolly 
the 
sheep 
was the 
first 
cloned 
mammal 


The three letters “DNA” have now become associated with crime solving, 
paternity testing, human identification, and genetic testing. DNA can be 
retrieved from hair, blood, or saliva. With the exception of identical twins, 
each person’s DNA is unique and it is possible to detect differences 
between human beings on the basis of their unique DNA sequence. 


DNA is the genetic material passed from parent to offspring for all life on 
Earth. The technology of molecular genetics developed in the last half 
century has enabled us to see deep into the history of life to deduce the 


relationships between living things in ways never thought possible. It also 
allows us to understand the workings of evolution in populations of 
organisms. Over a thousand species have had their entire genome 
sequenced, and there have been thousands of individual human genome 
sequences completed. These sequences will allow us to understand human 
disease and the relationship of humans to the rest of the tree of life. Finally, 
molecular genetics techniques have revolutionized plant and animal 
breeding for human agricultural needs. All of these advances in 
biotechnology depended on basic research leading to the discovery of the 
structure of DNA in 1953, and the research since then that has uncovered 
the details of DNA replication and the complex process leading to the 
expression of DNA in the form of proteins in the cell. 


Introduction Patterns Inheritance EnBio 
class="introduction" 


Experimentin 
g with 
thousands of 
garden peas, 
Mendel 
uncovered the 
fundamentals 
of genetics. 
(credit: 
modification 
of work by 
Jerry 
Kirkhart) 


Genetics is the study of heredity. Johann Gregor Mendel set the framework 
for genetics long before chromosomes or genes had been identified, at a 
time when meiosis was not well understood. Mendel selected a simple 
biological system and conducted methodical, quantitative analyses using 
large sample sizes. Because of Mendel’s work, the fundamental principles 
of heredity were revealed. We now know that genes, carried on 
chromosomes, are the basic functional units of heredity with the ability to 
be replicated, expressed, or mutated. Today, the postulates put forth by 
Mendel form the basis of classical, or Mendelian, genetics. Not all genes 
are transmitted from parents to offspring according to Mendelian genetics, 
but Mendel’s experiments serve as an excellent starting point for thinking 
about inheritance. 


Introduction Reproduction 2 EnBio 
class="introduction" 


Each of us, 
like these 
other large 
multicellula 
r organisms, 
begins life 
asa 
fertilized 
egg. After 
trillions of 
cell 
divisions, 
each of us 
develops 
into a 
complex, 
multicellula 
r organism. 
(credit a: 
modificatio 
n of work 
by Frank 
Wouters; 
credit b: 
modificatio 
n of work 
by Ken 
Cole, 
USGS; 
credit c: 
modificatio 
n of work 
by Martin 
Pettitt) 


The ability to reproduce in kind is a basic characteristic of all living things. 
In kind means that the offspring of any organism closely resembles its 
parent or parents. Hippopotamuses give birth to hippopotamus calves; 
Monterey pine trees produce seeds from which Monterey pine seedlings 
emerge; and adult flamingos lay eggs that hatch into flamingo chicks. In 
kind does not generally mean exactly the same. While many single-celled 
organisms and a few multicellular organisms can produce genetically 
identical clones of themselves through mitotic cell division, many single- 
celled organisms and most multicellular organisms reproduce regularly 
using another method. 


Sexual reproduction is the production by parents of haploid cells and the 
fusion of a haploid cell from each parent to form a single, unique diploid 
cell. In multicellular organisms, the new diploid cell will then undergo 
mitotic cell divisions to develop into an adult organism. A type of cell 
division called meiosis leads to the haploid cells that are part of the sexual 
reproductive cycle. Sexual reproduction, specifically meiosis and 
fertilization, introduces variation into offspring that may account for the 
evolutionary success of sexual reproduction. The vast majority of 
eukaryotic organisms can or must employ some form of meiosis and 
fertilization to reproduce. 


Introduction Reproduction EnBio 
class="introduction" 


A sea urchin 
begins life 
as a single 
cell that (a) 
divides to 

form two 
cells, visible 
by scanning 
electron 
microscopy. 
After four 
rounds of 
cell 

division, (b) 

there are 16 
cells, as 
seen in this 

SEM image. 
After many 
rounds of 

cell 
division, the 
individual 
develops 
into a 
complex, 
multicellula 

r organism, 
as seen in 

this (c) 
mature sea 
urchin. 
(credit a: 
modificatio 


n of work 
by Evelyn 
Spiegel, 
Louisa 
Howard; 
credit b: 
modificatio 
n of work 
by Evelyn 
Spiegel, 
Louisa 
Howard; 
credit c: 
modificatio 
n of work 
by Marco 
Busdraghi; 
scale-bar 
data from 


Matt 
Russell) 


(b) 


The individual sexually reproducing organism—including humans—begins 
life as a fertilized egg, or zygote. Trillions of cell divisions subsequently 
occur in a controlled manner to produce a complex, multicellular human. In 
other words, that original single cell was the ancestor of every other cell in 
the body. Once a human individual is fully grown, cell reproduction is still 


necessary to repair or regenerate tissues. For example, new blood and skin 
cells are constantly being produced. All multicellular organisms use cell 
division for growth, and in most cases, the maintenance and repair of cells 
and tissues. Single-celled organisms use cell division as their method of 
reproduction. 


Laws of Inheritance EnBio 
By the end of this section, you will be able to: 


e Explain the relationship between genotypes and phenotypes in 
dominant and recessive gene systems 

e Use a Punnett square to calculate the expected proportions of 
genotypes and phenotypes in a monohybrid cross 

e Explain Mendel’s law of segregation and independent assortment in 
terms of genetics and the events of meiosis 

e Explain the purpose and methods of a test cross 


The seven characteristics that Mendel evaluated in his pea plants were each 
expressed as one of two versions, or traits. Mendel deduced from his results 
that each individual had two discrete copies of the characteristic that are 
passed individually to offspring. We now call those two copies genes, which 
are carried on chromosomes. The reason we have two copies of each gene 
is that we inherit one from each parent. In fact, it is the chromosomes we 
inherit and the two copies of each gene are located on paired chromosomes. 
Recall that the separation, or segregation, of the homologous chromosomes 
means that only one of the copies of the gene gets moved into a gamete. 
The offspring are formed when that gamete unites with one from another 
parent and the two copies of each gene (and chromosome) are restored. 


For cases in which a single gene controls a single characteristic, a diploid 
organism has two genetic copies that may or may not encode the same 
version of that characteristic. For example, one individual may carry a gene 
that determines white flower color and a gene that determines violet flower 
color. Gene variants that arise by mutation and exist at the same relative 
locations on homologous chromosomes are called alleles. Mendel examined 
the inheritance of genes with just two allele forms, but it is common to 
encounter more than two alleles for any given gene in a natural population. 


Phenotypes and Genotypes 


Two alleles for a given gene in a diploid organism are expressed and 
interact to produce physical characteristics. The observable traits expressed 
by an organism are referred to as its phenotype. An organism’s underlying 


genetic makeup, consisting of both the physically visible and the non- 
expressed alleles, is called its genotype. Mendel’s hybridization 
experiments demonstrate the difference between phenotype and genotype. 
For example, the phenotypes that Mendel observed in his crosses between 
pea plants with differing traits are connected to the diploid genotypes of the 
plants in the P, F,, and F> generations. We will use a second trait that 
Mendel investigated, seed color, as an example. Seed color is governed by a 
single gene with two alleles. The yellow-seed allele is dominant and the 
green-seed allele is recessive. When true-breeding plants were cross- 
fertilized, in which one parent had yellow seeds and one had green seeds, 
all of the F, hybrid offspring had yellow seeds. That is, the hybrid offspring 
were phenotypically identical to the true-breeding parent with yellow seeds. 
However, we know that the allele donated by the parent with green seeds 
was not simply lost because it reappeared in some of the F> offspring 
({link]). Therefore, the F; plants must have been genotypically different 
from the parent with yellow seeds. 


The P plants that Mendel used in his experiments were each homozygous 
for the trait he was studying. Diploid organisms that are homozygous for a 
gene have two identical alleles, one on each of their homologous 
chromosomes. The genotype is often written as YY or yy, for which each 
letter represents one of the two alleles in the genotype. The dominant allele 
is capitalized and the recessive allele is lower case. The letter used for the 
gene (seed color in this case) is usually related to the dominant trait (yellow 
allele, in this case, or “Y”). Mendel’s parental pea plants always bred true 
because both produced gametes carried the same allele. When P plants with 
contrasting traits were cross-fertilized, all of the offspring were 
heterozygous for the contrasting trait, meaning their genotype had different 
alleles for the gene being examined. For example, the F; yellow plants that 
received a Y allele from their yellow parent and a y allele from their green 
parent had the genotype Yy. 


Phenotype 


[P] at @ 
(a) Cross-fertilization 


: 
100 percent 
[Fa] 


yellow progeny 
(hybrids) 


.) 


y (b) Self-fertilization 


‘*) 75 percent 

© yellow 
progeny 
25 percent 


green 
progeny 


Genotype 


YY yy 
| (a) Cross-fertilization 


1 
00 ae (yellow) 


uv (b) Self-fertilization 


25 percent 
WAC 
(yellow) 


50 percent 
Yy 


25 percent 


y } (green) 


Phenotypes are physical expressions of traits that 
are transmitted by alleles. Capital letters represent 
dominant alleles and lowercase letters represent 
recessive alleles. The phenotypic ratios are the 
ratios of visible characteristics. The genotypic 
ratios are the ratios of gene combinations in the 
offspring, and these are not always distinguishable 
in the phenotypes. 


Law of Dominance 


Our discussion of homozygous and heterozygous organisms brings us to 
why the F, heterozygous offspring were identical to one of the parents, 
rather than expressing both alleles. In all seven pea-plant characteristics, 
one of the two contrasting alleles was dominant, and the other was 
recessive. Mendel called the dominant allele the expressed unit factor; the 
recessive allele was referred to as the latent unit factor. We now know that 
these so-called unit factors are actually genes on homologous 
chromosomes. For a gene that is expressed in a dominant and recessive 


pattern, homozygous dominant and heterozygous organisms will look 
identical (that is, they will have different genotypes but the same 
phenotype), and the recessive allele will only be observed in homozygous 
recessive individuals ({link]). Mendel’s law of dominance states that in a 
heterozygote, one trait will conceal the presence of another trait for the 
same characteristic. 


Correspondence between Genotype and Phenotype for a 
Dominant-Recessive Characteristic. 


Homozygous Heterozygous Homozygous 
Genotype YY Yy yy 
Phenotype yellow yellow green 


Monohybrid Cross and the Punnett Square 


When fertilization occurs between two true-breeding parents that differ by 
only the characteristic being studied, the process is called a monohybrid 
cross, and the resulting offspring are called monohybrids. Mendel 
performed seven types of monohybrid crosses, each involving contrasting 
traits for different characteristics. Out of these crosses, all of the F, 
offspring had the phenotype of one parent, and the F, offspring had a 3:1 
phenotypic ratio. On the basis of these results, Mendel postulated that each 
parent in the monohybrid cross contributed one of two paired unit factors to 
each offspring, and every possible combination of unit factors was equally 
likely. 


The results of Mendel’s research can be explained in terms of probabilities, 
which are mathematical measures of likelihood. The probability of an event 
is calculated by the number of times the event occurs divided by the total 


number of opportunities for the event to occur. A probability of one (100 
percent) for some event indicates that it is guaranteed to occur, whereas a 
probability of zero (0 percent) indicates that it is guaranteed to not occur, 
and a probability of 0.5 (50 percent) means it has an equal chance of 
occurring or not occurring. 


To demonstrate this with a monohybrid cross, consider the case of true- 
breeding pea plants with yellow versus green seeds. The dominant seed 
color is yellow; therefore, the parental genotypes were YY for the plants 
with yellow seeds and yy for the plants with green seeds. A Punnett 
square, devised by the British geneticist Reginald Punnett, is useful for 
determining probabilities because it is drawn to predict all possible 
outcomes of all possible random fertilization events and their expected 
frequencies. [link] shows a Punnett square for a cross between a plant with 
yellow peas and one with green peas. To prepare a Punnett square, all 
possible combinations of the parental alleles (the genotypes of the gametes) 
are listed along the top (for one parent) and side (for the other parent) of a 
grid. The combinations of egg and sperm gametes are then made in the 
boxes in the table on the basis of which alleles are combining. Each box 
then represents the diploid genotype of a zygote, or fertilized egg. Because 
each possibility is equally likely, genotypic ratios can be determined from a 
Punnett square. If the pattern of inheritance (dominant and recessive) is 
known, the phenotypic ratios can be inferred as well. For a monohybrid 
cross of two true-breeding parents, each parent contributes one type of 
allele. In this case, only one genotype is possible in the F, offspring. All 
offspring are Yy and have yellow seeds. 


When the F, offspring are crossed with each other, each has an equal 
probability of contributing either a Y or a y to the F, offspring. The result is 
a 1 in 4 (25 percent) probability of both parents contributing a Y, resulting 
in an offspring with a yellow phenotype; a 25 percent probability of parent 
A contributing a Y and parent B ay, resulting in offspring with a yellow 
phenotype; a 25 percent probability of parent A contributing a y and parent 
B a, also resulting in a yellow phenotype; and a (25 percent) probability 
of both parents contributing a y, resulting in a green phenotype. When 
counting all four possible outcomes, there is a 3 in 4 probability of offspring 
having the yellow phenotype and a 1 in 4 probability of offspring having 


the green phenotype. This explains why the results of Mendel’s F> 
generation occurred in a 3:1 phenotypic ratio. Using large numbers of 
crosses, Mendel was able to calculate probabilities, found that they fit the 
model of inheritance, and use these to predict the outcomes of other crosses. 


Law of Segregation 


Observing that true-breeding pea plants with contrasting traits gave rise to 
F, generations that all expressed the dominant trait and F> generations that 
expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed 
the law of segregation. This law states that paired unit factors (genes) must 
segregate equally into gametes such that offspring have an equal likelihood 
of inheriting either factor. 


Test Cross 


Beyond predicting the offspring of a cross between known homozygous or 
heterozygous parents, Mendel also developed a way to determine whether 
an organism that expressed a dominant trait was a heterozygote or a 
homozygote. Called the test cross, this technique is still used by plant and 
animal breeders. In a test cross, the dominant-expressing organism is 
crossed with an organism that is homozygous recessive for the same 
characteristic. If the dominant-expressing organism is a homozygote, then 
all F, offspring will be heterozygotes expressing the dominant trait ({Link]). 
Alternatively, if the dominant-expressing organism is a heterozygote, the F, 
offspring will exhibit a 1:1 ratio of heterozygotes and recessive 
homozygotes ([link]). The test cross further validates Mendel’s postulate 
that pairs of unit factors segregate equally. 


A test cross can be performed to 
determine whether an organism 
expressing a dominant trait is a 
homozygote or a heterozygote. 


Law of Independent Assortment 


Mendel’s law of independent assortment states that genes do not 
influence each other with regard to the sorting of alleles into gametes, and 
every possible combination of alleles for every gene is equally likely to 
occur. Independent assortment of genes can be illustrated by the dihybrid 
cross, a cross between two true-breeding parents that express different traits 
for two characteristics. Consider the characteristics of seed color and seed 


texture for two pea plants, one that has wrinkled, green seeds (rryy) and 
another that has round, yellow seeds (RRYY). Because each parent is 
homozygous, the law of segregation indicates that the gametes for the 
wrinkled—green plant all are ry, and the gametes for the round—yellow plant 
are all RY. Therefore, the F, generation of offspring all are RrYy ([link]). 


Note: 
Art Connection 


A dihybrid cross in pea plants involves the genes 
for seed color and texture. The P cross produces 
F, offspring that are all heterozygous for both 
characteristics. The resulting 9:3:3:1 F> 
phenotypic ratio is obtained using a Punnett 
square. 


In pea plants, purple flowers (P) are dominant to white (p), and yellow 
peas (Y) are dominant to green (y). What are the possible genotypes and 
phenotypes for a cross between PpYY and ppYy pea plants? How many 
squares would you need to complete a Punnett square analysis of this 
cross? 


The gametes produced by the F individuals must have one allele from each 
of the two genes. For example, a gamete could get an R allele for the seed 
shape gene and either a Y or ay allele for the seed color gene. It cannot get 
both an R and an r allele; each gamete can have only one allele per gene. 
The law of independent assortment states that a gamete into which an r 
allele is sorted would be equally likely to contain either a Y or ay allele. 
Thus, there are four equally likely gametes that can be formed when the 
RrYy heterozygote is self-crossed, as follows: RY, rY, Ry, and ry. Arranging 
these gametes along the top and left of a 4 x 4 Punnett square ([link]) gives 
us 16 equally likely genotypic combinations. From these genotypes, we find 
a phenotypic ratio of 9 round—yellow:3 round—green:3 wrinkled—yellow:1 
wrinkled—green ([link]). These are the offspring ratios we would expect, 
assuming we performed the crosses with a large enough sample size. 


Section Summary 


When true-breeding, or homozygous, individuals that differ for a certain 
trait are crossed, all of the offspring will be heterozygous for that trait. If the 
traits are inherited as dominant and recessive, the F, offspring will all 
exhibit the same phenotype as the parent homozygous for the dominant 
trait. If these heterozygous offspring are self-crossed, the resulting F>5 
offspring will be equally likely to inherit gametes carrying the dominant or 
recessive trait, giving rise to offspring of which one quarter are 
homozygous dominant, half are heterozygous, and one quarter are 
homozygous recessive. Because homozygous dominant and heterozygous 
individuals are phenotypically identical, the observed traits in the F> 
offspring will exhibit a ratio of three dominant to one recessive. 


Mendel postulated that genes (characteristics) are inherited as pairs of 
alleles (traits) that behave in a dominant and recessive pattern. Alleles 
segregate into gametes such that each gamete is equally likely to receive 
either one of the two alleles present in a diploid individual. In addition, 
genes are assorted into gametes independently of one another. That is, in 
general, alleles are not more likely to segregate into a gamete with a 
particular allele of another gene. 


Glossary 


allele 
one of two or more variants of a gene that determines a particular trait 
for a characteristic 


dihybrid 
the result of a cross between two true-breeding parents that express 
different traits for two characteristics 


genotype 
the underlying genetic makeup, consisting of both physically visible 


and non-expressed alleles, of an organism 


heterozygous 
having two different alleles for a given gene on the homologous 
chromosomes 


homozygous 
having two identical alleles for a given gene on the homologous 
chromosomes 


law of dominance 
in a heterozygote, one trait will conceal the presence of another trait 
for the same characteristic 


law of independent assortment 
genes do not influence each other with regard to sorting of alleles into 
gametes; every possible combination of alleles is equally likely to 
occur 


law of segregation 
paired unit factors (i.e., genes) segregate equally into gametes such 
that offspring have an equal likelihood of inheriting any combination 
of factors 


monohybrid 
the result of a cross between two true-breeding parents that express 
different traits for only one characteristic 


phenotype 
the observable traits expressed by an organism 


Punnett square 
a visual representation of a cross between two individuals in which the 
gametes of each individual are denoted along the top and side of a 
grid, respectively, and the possible zygotic genotypes are recombined 
at each box in the grid 


test cross 
a cross between a dominant expressing individual with an unknown 
genotype and a homozygous recessive individual; the offspring 
phenotypes indicate whether the unknown parent is heterozygous or 
homozygous for the dominant trait 


Mendel’s Experiments EnBio 
By the end of this section, you will be able to: 


e Explain the scientific reasons for the success of Mendel’s experimental 
work 

¢ Describe the expected outcomes of monohybrid crosses involving 
dominant and recessive alleles 


Johann Gregor Mendel 
set the framework for 
the study of genetics. 


Johann Gregor Mendel (1822-1884) ([{link]) was a lifelong learner, teacher, 
scientist, and man of faith. In 1865, Mendel presented the results of his 
experiments with nearly 30,000 pea plants to the local natural history 
society. He demonstrated that traits are transmitted faithfully from parents 
to offspring in specific patterns. 


Mendel’s work went virtually unnoticed by the scientific community, which 
incorrectly believed that the process of inheritance involved a blending of 
parental traits that produced an intermediate physical appearance in 
offspring. This hypothetical process appeared to be correct because of what 
we know now as continuous variation. Continuous variation is the range 


of small differences we see among individuals in a characteristic like 
human height. It does appear that offspring are a “blend” of their parents’ 
traits when we look at characteristics that exhibit continuous variation. 
Mendel worked instead with traits that show discontinuous variation. 
Discontinuous variation is the variation seen among individuals when each 
individual shows one of two—or a very few—easily distinguishable traits, 
such as violet or white flowers. 


Mendel’s Crosses 


Mendel’s seminal work was accomplished using the garden pea, Pisum 
sativum, to study inheritance. “True-breeding,” pea plants are plants that 
always produce offspring that look like the parent. Large quantities of 
garden peas could be cultivated simultaneously, allowing Mendel to 
conclude that his results did not come about simply by chance. 


Mendel performed hybridizations, which involve mating two true-breeding 
individuals that have different traits. In the pea, which is naturally self- 
pollinating, this is done by manually transferring pollen from the anther of a 
mature pea plant of one variety to the stigma of a separate mature pea plant 
of the second variety. 


Plants used in first-generation crosses were called P, or parental generation, 
plants ([link]). Mendel collected the seeds produced by the P plants that 
resulted from each cross and grew them the following season. These 
offspring were called the Fj, or the first filial (filial = daughter or son), 
generation. Once Mendel examined the characteristics in the F; generation 
of plants, he allowed them to self-fertilize naturally. He then collected and 
grew the seeds from the F, plants to produce the Fy, or second filial, 
generation. Mendel’s experiments extended beyond the F>, generation to the 
F3 generation, F, generation, and so on, but it was the ratio of 
characteristics in the P, F;, and F> generations that were the most intriguing 
and became the basis of Mendel’s postulates. 


Hybridization of true-breeding plants 


Self-fertilization of hybrid plants 


Mendel’s process for performing 
crosses included examining flower 
color. 


Garden Pea Characteristics Revealed the Basics of Heredity 


In his 1865 publication, Mendel reported the results of his crosses involving 
seven different characteristics, each with two contrasting traits. A trait is 
defined as a variation in the physical appearance of a heritable 
characteristic. The characteristics included plant height, seed texture, seed 
color, flower color, pea-pod size, pea-pod color, and flower position. For 
the characteristic of flower color, for example, the two contrasting traits 
were white versus violet. To fully examine each characteristic, Mendel 
generated large numbers of F, and F> plants and reported results from 
thousands of F> plants. 


Once he was sure he had true-breeding plants, Mendel applied the pollen 
from a plant with violet flowers to the stigma of a plant with white flowers. 
After gathering and sowing the seeds that resulted from this cross, Mendel 
found that 100 percent of the F; hybrid generation had violet flowers. 
Conventional wisdom at that time would have predicted the hybrid flowers 
to be pale violet or for hybrid plants to have equal numbers of white and 
violet flowers. In other words, the contrasting parental traits were expected 
to blend in the offspring. Instead, Mendel’s results demonstrated that the 
white flower trait had completely disappeared in the F, generation. 


Importantly, Mendel did not stop his experimentation there. He allowed the 
F, plants to self-fertilize and found that 705 plants in the F> generation had 
violet flowers and 224 had white flowers. This was a ratio of 3.15 violet 
flowers to one white flower, or approximately 3:1. When Mendel 
transferred pollen from a plant with violet flowers to the stigma of a plant 
with white flowers and vice versa, he obtained approximately the same ratio 
irrespective of which parent—male or female—contributed which trait. 
This is called a reciprocal cross—a paired cross in which the respective 
traits of the male and female in one cross become the respective traits of the 
female and male in the other cross. For the other six characteristics that 
Mendel examined, the F, and F> generations behaved in the same way that 
they behaved for flower color. One of the two traits would disappear 
completely from the F, generation, only to reappear in the F> generation at 
a ratio of roughly 3:1 ([{link])). 


Seed shape 


© 


@ 


Round Wrinkled 
Seed color ~) we 
Flower position 
Yellow Green 


Flower color Terminal 


% 


ae 


Purple White 


Pod shape Jf Jf 
Inflated Constricted 
Stem height 
Pod color 
Yellow Green Tall Dwarf 


Mendel identified seven pea plant characteristics. 


Upon compiling his results for many thousands of plants, Mendel 
concluded that the characteristics could be divided into expressed and latent 
traits. He called these dominant and recessive traits, respectively. 
Dominant traits are those that are inherited unchanged in a hybridization. 
Recessive traits become latent, or disappear in the offspring of a 
hybridization. The recessive trait does, however, reappear in the progeny of 
the hybrid offspring. An example of a dominant trait is the violet-colored 
flower trait. For this same characteristic (flower color), white-colored 
flowers are a recessive trait. The fact that the recessive trait reappeared in 
the Fy generation meant that the traits remained separate (and were not 
blended) in the plants of the F; generation. Mendel proposed that this was 
because the plants possessed two copies of the trait for the flower-color 
characteristic, and that each parent transmitted one of their two copies to 
their offspring, where they came together. Moreover, the physical 
observation of a dominant trait could mean that the genetic composition of 
the organism included two dominant versions of the characteristic, or that it 


included one dominant and one recessive version. Conversely, the 
observation of a recessive trait meant that the organism lacked any 
dominant versions of this characteristic. 


Note: 
Concept in Action 


Baan 


wees OPenstax COLLEGE” 


cout 


For an excellent review of Mendel’s experiments and to perform your own 
crosses and identify patterns of inheritance, visit the Mendel’s Peas web 
lab. 


Section Summary 


Working with garden pea plants, Mendel found that crosses between parents 
that differed for one trait produced F, offspring that all expressed one 
parent’s traits. The traits that were visible in the F, generation are referred 
to as dominant, and traits that disappear in the F; generation are described 
as recessive. When the F, plants in Mendel’s experiment were self-crossed, 
the F, offspring exhibited the dominant trait or the recessive trait in a 3:1 
ratio, confirming that the recessive trait had been transmitted faithfully from 
the original P parent. Reciprocal crosses generated identical F; and F> 
offspring ratios. By examining sample sizes, Mendel showed that traits 
were inherited as independent events. 


Glossary 


continuous variation 


a variation in a characteristic in which individuals show a range of 
traits with small differences between them 


discontinuous variation 
a variation in a characteristic in which individuals show two, or a few, 
traits with large differences between them 


dominant 
describes a trait that masks the expression of another trait when both 
versions of the gene are present in an individual 


the first filial generation in a cross; the offspring of the parental 
generation 


Fy 
the second filial generation produced when F;, individuals are self- 
crossed or fertilized with each other 


hybridization 
the process of mating two individuals that differ, with the goal of 
achieving a certain characteristic in their offspring 


model system 
a species or biological system used to study a specific biological 
phenomenon to gain understanding that will be applied to other species 


the parental generation in a cross 


recessive 
describes a trait whose expression is masked by another trait when the 
alleles for both traits are present in an individual 


reciprocal cross 
a paired cross in which the respective traits of the male and female in 
one cross become the respective traits of the female and male in the 
other cross 


trait 
a variation in an inherited characteristic 


Photosynthesis EnBio 
By the end of this section, you will be able to: 


e¢ Summarize the process of photosynthesis 

e Explain the relevance of photosynthesis to other living things 
e Identify the reactants and products of photosynthesis 

e Describe the main structures involved in photosynthesis 


All living organisms on earth consist of one or more cells. Each cell runs on 
the chemical energy found mainly in carbohydrate molecules (food), and 
the majority of these molecules are produced by one process: 
photosynthesis. Through photosynthesis, certain organisms convert solar 
energy (sunlight) into chemical energy, which is then used to build 
carbohydrate molecules. The energy used to hold these molecules together 
is released when an organism breaks down food. Cells then use this energy 
to perform work, such as cellular respiration. 


The energy that is harnessed from photosynthesis enters the ecosystems of 
our planet continuously and is transferred from one organism to another. 
Therefore, directly or indirectly, the process of photosynthesis provides 
most of the energy required by living things on earth. 


Photosynthesis also results in the release of oxygen into the atmosphere. In 
short, to eat and breathe, humans depend almost entirely on the organisms 
that carry out photosynthesis. 


Note: 
Concept in Action 


Click the following link to learn more about photosynthesis. 


Solar Dependence and Food Production 


Some organisms can carry out photosynthesis, whereas others cannot. An 
autotroph is an organism that can produce its own food. The Greek roots of 
the word autotroph mean “self” (auto) “feeder” (troph). Plants are the best- 
known autotrophs, but others exist, including certain types of bacteria and 
algae ([link]). Oceanic algae contribute enormous quantities of food and 
oxygen to global food chains. Plants are also photoautotrophs, a type of 
autotroph that uses sunlight and carbon from carbon dioxide to synthesize 
chemical energy in the form of carbohydrates. All organisms carrying out 
photosynthesis require sunlight. 


(a) (b) (c) 


(a) Plants, (b) algae, and (c) certain bacteria, called cyanobacteria, are 
photoautotrophs that can carry out photosynthesis. Algae can grow 
over enormous areas in water, at times completely covering the 
surface. (credit a: Steve Hillebrand, U.S. Fish and Wildlife Service; 
credit b: "eutrophication&hypoxia"/Flickr; credit c: NASA; scale-bar 
data from Matt Russell) 


Heterotrophs are organisms incapable of photosynthesis that must 
therefore obtain energy and carbon from food by consuming other 
organisms. The Greek roots of the word heterotroph mean “other” (hetero) 


“feeder” (troph), meaning that their food comes from other organisms. Even 
if the food organism is another animal, this food traces its origins back to 
autotrophs and the process of photosynthesis. Humans are heterotrophs, as 
are all animals. Heterotrophs depend on autotrophs, either directly or 
indirectly. Deer and wolves are heterotrophs. A deer obtains energy by 
eating plants. A wolf eating a deer obtains energy that originally came from 
the plants eaten by that deer. The energy in the plant came from 
photosynthesis, and therefore it is the only autotroph in this example 
({link]). Using this reasoning, all food eaten by humans also links back to 
autotrophs that carry out photosynthesis. 


The energy stored in carbohydrate 
molecules from photosynthesis passes 
through the food chain. The predator 
that eats these deer is getting energy 
that originated in the photosynthetic 
vegetation that the deer consumed. 
(credit: Steve VanRiper, U.S. Fish and 
Wildlife Service) 


Main Structures and Summary of Photosynthesis 


Photosynthesis requires sunlight, carbon dioxide, and water as starting 
reactants ({link]). After the process is complete, photosynthesis releases 
oxygen and produces carbohydrate molecules, most commonly glucose. 
These sugar molecules contain the energy that living things need to survive. 


——_— 


- PHOTOSYNTHESIS 


Photosynthesis uses solar energy, 
carbon dioxide, and water to release 
oxygen and to produce energy-storing 
sugar molecules. 


The complex reactions of photosynthesis can be summarized by the 
chemical equation shown in [link]. 


Photosynthesis Equation 


SUNLIGHT 


Carbon 
dioxide * Water == Sugar + Oxygen 


The process of photosynthesis can be 
represented by an equation, wherein carbon 
dioxide and water produce sugar and oxygen 
using energy from sunlight. 


In plants, photosynthesis takes place primarily in leaves, which consist of 
many layers of cells and have differentiated top and bottom sides. The 
process of photosynthesis occurs not on the surface layers of the leaf, but 
rather in a middle layer called the mesophyll ((link]). The gas exchange of 
carbon dioxide and oxygen occurs through small, regulated openings called 
stomata. 


In all autotrophic eukaryotes, photosynthesis takes place inside an organelle 
called a chloroplast. In plants, chloroplast-containing cells exist in the 
mesophyll. Other types of pigments are also involved in photosynthesis, but 
chlorophyll is by far the most important. 


Note: 
Art Connection 


Mesophyll 


Stomata x 


Chloroplast 


x 
IN Thylakoids 


Not all cells of a leaf carry out 
photosynthesis. Cells within the 
middle layer of a leaf have 
chloroplasts, which contain the 
photosynthetic apparatus. (credit 
"leaf": modification of work by Cory 
Zanker) 


On a hot, dry day, plants close their stomata to conserve water. What 


impact will this have on photosynthesis? 


Section Summary 


The process of photosynthesis transformed life on earth. By harnessing 
energy from the sun, photosynthesis allowed living things to access 
enormous amounts of energy. Because of photosynthesis, living things 
gained access to sufficient energy, allowing them to evolve new structures 
and achieve the biodiversity that is evident today. 


Only certain organisms, called autotrophs, can perform photosynthesis; they 
require the presence of chlorophyll, a specialized pigment that can absorb 
light and convert light energy into chemical energy. Photosynthesis uses 
carbon dioxide and water to assemble carbohydrate molecules (usually 
glucose) and releases oxygen into the air. Eukaryotic autotrophs, such as 
plants and algae, have organelles called chloroplasts in which 
photosynthesis takes place. 


Glossary 


autotroph 
an organism capable of producing its own food 


chlorophyll 
the green pigment that captures the light energy that drives the 
reactions of photosynthesis 


chloroplast 
the organelle where photosynthesis takes place 


granum 
a stack of thylakoids located inside a chloroplast 


heterotroph 
an organism that consumes other organisms for food 


light-dependent reaction 
the first stage of photosynthesis where visible light is absorbed to form 
two energy-carrying molecules (ATP and NADPH) 


mesophyll 
the middle layer of cells in a leaf 


photoautotroph 
an organism capable of synthesizing its own food molecules (storing 
energy), using the energy of light 


pigment 
a molecule that is capable of absorbing light energy 


stoma 
the opening that regulates gas exchange and water regulation between 
leaves and the environment; plural: stomata 


stroma 
the fluid-filled space surrounding the grana inside a chloroplast where 
the Calvin cycle reactions of photosynthesis take place 


thylakoid 
a disc-shaped membranous structure inside a chloroplast where the 
light-dependent reactions of photosynthesis take place using 
chlorophyll embedded in the membranes 


Population Demographics and Dynamics EnBio 
By the end of this section, you will be able to: 


e Describe how ecologists measure population size and density 

e Describe three different patterns of population distribution 

e Use life tables to calculate mortality rates 

e Describe the three types of survivorship curves and relate them to 
specific populations 


Populations are dynamic entities. Their size and composition fluctuate in 
response to numerous factors, including seasonal and yearly changes in the 
environment, natural disasters such as forest fires and volcanic eruptions, 
and competition for resources between and within species. The statistical 
study of populations is called demography: a set of mathematical tools 
designed to describe populations and investigate how they change. Many of 
these tools were actually designed to study human populations. For example, 
life tables, which detail the life expectancy of individuals within a 
population, were initially developed by life insurance companies to set 
insurance rates. In fact, while the term “demographics” is sometimes 
assumed to mean a study of human populations, all living populations can 
be studied using this approach. 


Population Size and Density 


Populations are characterized by their population size (total number of 
individuals) and their population density (number of individuals per unit 
area). A population may have a large number of individuals that are 
distributed densely, or sparsely. There are also populations with small 
numbers of individuals that may be dense or very sparsely distributed in a 
local area. Population size can affect potential for adaptation because it 
affects the amount of genetic variation present in the population. Density 
can have effects on interactions within a population such as competition for 
food and the ability of individuals to find a mate. Smaller organisms tend to 
be more densely distributed than larger organisms ({link]). 


Note: 


Art Connection 


Relationship between Population and Body Mass in Australian Mammals 


Quoll 

Bandicoot 
Wombat 
Rat-kangaroo 
Potoroo 
Possom species 
Tree kangaroo 


N 
° 


Log density (km?) 


Pr 
o 


Kangaroo 
Bear cuscus 
Glider species 


e 
. 
A 
e 
x 
° 
a 
A 
° 
x 


2.0 3.0 
Log mass (grams) 


Australian mammals show a typical 
inverse relationship between population 
density and body size. 


As this graph shows, population density typically decreases with increasing 
body size. Why do you think this is the case? 


Estimating Population Size 


The most accurate way to determine population size is to count all of the 
individuals within the area. However, this method is usually not logistically 
or economically feasible, especially when studying large areas. Thus, 
scientists usually study populations by sampling a representative portion of 
each habitat and use this sample to make inferences about the population as 
a whole. The methods used to sample populations to determine their size 
and density are typically tailored to the characteristics of the organism being 
studied. For immobile organisms such as plants, or for very small and slow- 
moving organisms, a quadrat may be used. A quadrat is a wood, plastic, or 
metal square that is placed on the ground to describe a given area. 


For smaller mobile organisms, such as mammals or fish, a technique called 
mark and recapture is often used. This method involves marking a sample 
of captured animals in some way and releasing them back into the 
environment to mix with the rest of the population; then, a new sample is 
captured and scientists determine how many of the marked animals are in 
the new sample. This method assumes that the larger the population, the 
lower the percentage of marked organisms that will be recaptured since they 
will have mixed with more unmarked individuals. For example, if 80 field 
mice are captured, marked, and released into the forest, then a second 
trapping 100 field mice are captured and 20 of them are marked, the 
population size (N) can be determined using the following equation: 
Equation: 


number marked first catch x total number second catch _wNn 
number marked second catch — 


Using our example, the population size would be 400. 
Equation: 


80 x 100 


= 4 
20 00 


These results give us an estimate of 400 total individuals in the original 
population. The true number usually will be a bit different from this because 
of chance errors and possible bias caused by the sampling methods. 


Species Distribution 


In addition to measuring density, further information about a population can 
be obtained by looking at the distribution of the individuals throughout their 
range. A species distribution pattern is the distribution of individuals 
within a habitat at a particular point in time—broad categories of patterns 
are used to describe them. 


Individuals within a population can be distributed at random, in groups, or 
equally spaced apart (more or less). These are known as random, clumped, 


and uniform distribution patterns, respectively ((link]). An example of 
random distribution occurs with dandelion and other plants that have wind- 
dispersed seeds that germinate wherever they happen to fall in favorable 
environments. A clumped distribution, may be seen in plants that drop their 
seeds straight to the ground, such as oak trees; it can also be seen in animals 
that live in social groups (schools of fish or herds of elephants). Uniform 
distribution is observed in plants that secrete substances inhibiting the 
growth of nearby individuals (such as the release of toxic chemicals by sage 
plants). It is also seen in territorial animal species, such as penguins that 
maintain a defined territory for nesting. The territorial defensive behaviors 
of each individual create a regular pattern of distribution of similar-sized 
territories and individuals within those territories. Thus, the distribution of 
the individuals within a population provides more information about how 
they interact with each other than does a simple density measurement. 


Clumped Uniform 


(a) (b) () 


Species may have a random, clumped, or uniform distribution. 
Plants such as (a) dandelions with wind-dispersed seeds tend to 
be randomly distributed. Animals such as (b) elephants that 
travel in groups exhibit a clumped distribution. Territorial birds 
such as (c) penguins tend to have a uniform distribution. (credit 
a: modification of work by Rosendahl; credit b: modification of 
work by Rebecca Wood; credit c: modification of work by Ben 
Tubby) 


Demography 


While population size and density describe a population at one particular 
point in time, scientists must use demography to study the dynamics of a 
population. Demography is the statistical study of population changes over 
time: birth rates, death rates, and life expectancies. These population 
characteristics are often displayed in a life table. 


Life Tables 


Life tables provide important information about the life history of an 
organism and the life expectancy of individuals at each age. They are 
modeled after actuarial tables used by the insurance industry for estimating 
human life expectancy. Life tables may include the probability of each age 
group dying before their next birthday, the percentage of surviving 
individuals dying at a particular age interval (their mortality rate, and their 
life expectancy at each interval. An example of a life table is shown in [link] 
from a study of Dall mountain sheep, a species native to northwestern North 
America. Notice that the population is divided into age intervals (column 
A). The mortality rate (per 1000) shown in column D is based on the 
number of individuals dying during the age interval (column B), divided by 
the number of individuals surviving at the beginning of the interval (Column 
C) multiplied by 1000. 

Equation: 


number of individuals dying 


mortality rate = x 1000 


number of individuals surviving 


For example, between ages three and four, 12 individuals die out of the 776 
that were remaining from the original 1000 sheep. This number is then 
multiplied by 1000 to give the mortality rate per thousand. 

Equation: 


12 
li = — 1 ~ 15. 
mortality rate 776 x 1000 5.5 


As can be seen from the mortality rate data (column D), a high death rate 
occurred when the sheep were between six months and a year old, and then 
increased even more from 8 to 12 years old, after which there were few 
survivors. The data indicate that if a sheep in this population were to survive 
to age one, it could be expected to live another 7.7 years on average, as 
shown by the life-expectancy numbers in column E. 


Life Table of Dall Mountain Sheep! 


footnote] 


Data Adapted from Edward S. Deevey, Jr., “Life Tables for Natural 
Populations of Animals,” The Quarterly Review of Biology 22, no. 4 
(December 1947): 283-314. 


A 


Age 
interval 
(years) 


0-0.5 
0.5-1 
1-2 


2-3 


B 


Number 
dying in 
age 
interval 
out of 
1000 
born 


34 
145 
12 


13 


C 


Number 
surviving 
at 
beginning 
of age 
interval 
out of 
1000 
born 


1000 
946 
801 


789 


D 


Mortality 
rate per 
1000 alive 
at 
beginning 
of age 
interval 


54.0 
153.3 
15.0 


16.5 


E 


Life 
expectancy 
or mean 
lifetime 
remaining 
to those 
attaining 
age 
interval 


7.06 


VET 


6.8 


3-4 12 776 15.5 5.9 


4-5 30 764 39.3 5.0 
5-6 46 734 62.7 4.2 
6—7 48 688 69.8 3.4 
7-8 69 640 107.8 2.6 
8-9 132 971 251.2 i 
9-10 187 439 426.0 1.3 
10-11 156 252 619.0 0.9 
11-12 90 96 937.5 0.6 
12-13 3 6 500.0 1.2 
13-14 3 3 1000 0.7 


This life table of Ovis dalli shows the number of deaths, number of survivors, 
mortality rate, and life expectancy at each age interval for Dall mountain 
sheep. 


Survivorship Curves 


Another tool used by population ecologists is a survivorship curve, which 
is a graph of the number of individuals surviving at each age interval versus 
time. These curves allow us to compare the life histories of different 
populations ({link]). There are three types of survivorship curves. In a type I 
curve, mortality is low in the early and middle years and occurs mostly in 
older individuals. Organisms exhibiting a type I survivorship typically 
produce few offspring and provide good care to the offspring increasing the 


likelihood of their survival. Humans and most mammals exhibit a type I 
survivorship curve. In type II curves, mortality is relatively constant 
throughout the entire life span, and mortality is equally likely to occur at any 
point in the life span. Many bird populations provide examples of an 
intermediate or type II survivorship curve. In type III survivorship curves, 
early ages experience the highest mortality with much lower mortality rates 
for organisms that make it to advanced years. Type III organisms typically 
produce large numbers of offspring, but provide very little or no care for 
them. Trees and marine invertebrates exhibit a type III survivorship curve 
because very few of these organisms survive their younger years, but those 
that do make it to an old age are more likely to survive for a relatively long 
period of time. 


Survivorship Curve 


Type | (humans) ¢ 


Type Ill (trees) 


> 
2 
oo) 
oO 
n 
D> 
2 
= 
D 
£ 
2 
2 
S 
n 
2 
o 
=] 
3 
i 
x] 
.= 
= 
S 
Pa 
a) 
a2 
E 
=i 
Zz 


Survivorship curves show the 
distribution of individuals in a 
population according to age. 
Humans and most mammals have 
a Type I survivorship curve, 
because death primarily occurs in 
the older years. Birds have a Type 
II survivorship curve, as death at 
any age is equally probable. Trees 


have a Type III survivorship curve 
because very few survive the 
younger years, but after a certain 
age, individuals are much more 
likely to survive. 


Section Summary 


Populations are individuals of a species that live in a particular habitat. 
Ecologists measure characteristics of populations: size, density, and 
distribution pattern. Life tables are useful to calculate life expectancies of 
individual population members. Survivorship curves show the number of 
individuals surviving at each age interval plotted versus time. 


Glossary 


demography 
the statistical study of changes in populations over time 


life table 
a table showing the life expectancy of a population member based on 
its age 


mark and recapture 
a method used to determine population size in mobile organisms 


mortality rate 
the proportion of population surviving to the beginning of an age 
interval that dies during that age interval 


population density 
the number of population members divided by the area being measured 


population size 
the number of individuals in a population 


quadrat 
a square within which a count of individuals is made that is combined 
with other such counts to determine population size and density in slow 
moving or stationary organisms 


species distribution pattern 
the distribution of individuals within a habitat at a given point in time 


survivorship curve 
a graph of the number of surviving population members versus the 
relative age of the member 


Population Growth and Regulation EnBio 
By the end of this section, you will be able to: 


e Explain the characteristics of and differences between exponential and 
logistic growth patterns 

e Give examples of exponential and logistic growth in natural 
populations 

e Give examples of how the carrying capacity of a habitat may change 

e Compare and contrast density-dependent growth regulation and 
density-independent growth regulation giving examples 


Population ecologists make use of a variety of methods to model population 
dynamics. An accurate model should be able to describe the changes 
occurring in a population and predict future changes. 


Population Growth 


The two simplest models of population growth use deterministic equations 
(equations that do not account for random events) to describe the rate of 
change in the size of a population over time. The first of these models, 
exponential growth, describes theoretical populations that increase in 
numbers without any limits to their growth. The second model, logistic 
growth, introduces limits to reproductive growth that become more intense 
as the population size increases. Neither model adequately describes natural 
populations, but they provide points of comparison. 


Exponential Growth 


Charles Darwin, in developing his theory of natural selection, was 
influenced by the English clergyman Thomas Malthus. Malthus published 
his book in 1798 stating that populations with abundant natural resources 
grow very rapidly; however, they limit further growth by depleting their 
resources. The early pattern of accelerating population size is called 
exponential growth. 


The best example of exponential growth in organisms is seen in bacteria. 
Bacteria are prokaryotes that reproduce largely by binary fission. This 
division takes about an hour for many bacterial species. If 1000 bacteria are 
placed in a large flask with an abundant supply of nutrients (so the nutrients 
will not become quickly depleted), the number of bacteria will have 
doubled from 1000 to 2000 after just an hour. In another hour, each of the 
2000 bacteria will divide, producing 4000 bacteria. After the third hour, 
there should be 8000 bacteria in the flask. The important concept of 
exponential growth is that the growth rate—the number of organisms added 
in each reproductive generation—is itself increasing; that is, the population 
size is increasing at a greater and greater rate. After 24 of these cycles, the 
population would have increased from 1000 to more than 16 billion 
bacteria. When the population size, N, is plotted over time, a J-shaped 
growth curve is produced ([link]a). 


The bacteria-in-a-flask example is not truly representative of the real world 
where resources are usually limited. However, when a species is introduced 
into a new habitat that it finds suitable, it may show exponential growth for 
a while. In the case of the bacteria in the flask, some bacteria will die during 
the experiment and thus not reproduce; therefore, the growth rate is lowered 
from a maximal rate in which there is no mortality. The growth rate of a 
population is largely determined by subtracting the death rate, D, (number 
organisms that die during an interval) from the birth rate, B, (number 
organisms that are born during an interval). The growth rate can be 
expressed in a simple equation that combines the birth and death rates into a 
single factor: r. This is shown in the following formula: 

Equation: 


Population growth = rN 


The value of r can be positive, meaning the population is increasing in size 
(the rate of change is positive); or negative, meaning the population is 
decreasing in size; or zero, in which case the population size is unchanging, 
a condition known as zero population growth. 


Logistic Growth 


Extended exponential growth is possible only when infinite natural 
resources are available; this is not the case in the real world. Charles 
Darwin recognized this fact in his description of the “struggle for 
existence,” which states that individuals will compete (with members of 
their own or other species) for limited resources. The successful ones are 
more likely to survive and pass on the traits that made them successful to 
the next generation at a greater rate (natural selection). To model the reality 
of limited resources, population ecologists developed the logistic growth 
model. 


Carrying Capacity and the Logistic Model 


In the real world, with its limited resources, exponential growth cannot 
continue indefinitely. Exponential growth may occur in environments where 
there are few individuals and plentiful resources, but when the number of 
individuals gets large enough, resources will be depleted and the growth 
rate will slow down. Eventually, the growth rate will plateau or level off 
({link]b). This population size, which is determined by the maximum 
population size that a particular environment can sustain, is called the 
carrying capacity, or K. In real populations, a growing population often 
overshoots its carrying capacity, and the death rate increases beyond the 
birth rate causing the population size to decline back to the carrying 
capacity or below it. Most populations usually fluctuate around the carrying 
capacity in an undulating fashion rather than existing right at it. 


The formula used to calculate logistic growth adds the carrying capacity as 
a moderating force in the growth rate. The expression “K — N” is equal to 
the number of individuals that may be added to a population at a given time, 
and “K — N” divided by “K” is the fraction of the carrying capacity 
available for further growth. Thus, the exponential growth model is 
restricted by this factor to generate the logistic growth equation: 

Equation: 


| 


Population growth = rN K 


Notice that when N is almost zero the quantity in brackets is almost equal to 
1 (or K/K) and growth is close to exponential. When the population size is 
equal to the carrying capacity, or N = K, the quantity in brackets is equal to 
zero and growth is equal to zero. A graph of this equation (logistic growth) 
yields the S-shaped curve ([link]b). It is a more realistic model of 
population growth than exponential growth. There are three different 
sections to an S-shaped curve. Initially, growth is exponential because there 
are few individuals and ample resources available. Then, as resources begin 
to become limited, the growth rate decreases. Finally, the growth rate levels 
off at the carrying capacity of the environment, with little change in 
population number over time. 


o oO 
N N 
77) w 
Cc Cc 
Ss S 
& & 
=] a 
a a. 
fo) jo) 
a a 


(a) (b) 


When resources are unlimited, populations exhibit 
(a) exponential growth, shown in a J-shaped curve. 
When resources are limited, populations exhibit 
(b) logistic growth. In logistic growth, population 
expansion decreases as resources become scarce, 
and it levels off when the carrying capacity of the 
environment is reached. The logistic growth curve 
is S-shaped. 


Role of Intraspecific Competition 


The logistic model assumes that every individual within a population will 
have equal access to resources and, thus, an equal chance for survival. For 
plants, the amount of water, sunlight, nutrients, and space to grow are the 
important resources, whereas in animals, important resources include food, 
water, shelter, nesting space, and mates. 


In the real world, phenotypic variation among individuals within a 
population means that some individuals will be better adapted to their 
environment than others. The resulting competition for resources among 
population members of the same species is termed intraspecific 
competition. Intraspecific competition may not affect populations that are 
well below their carrying capacity, as resources are plentiful and all 
individuals can obtain what they need. However, as population size 
increases, this competition intensifies. In addition, the accumulation of 
waste products can reduce carrying capacity in an environment. 


Examples of Logistic Growth 


Yeast, a microscopic fungus used to make bread and alcoholic beverages, 
exhibits the classical S-shaped curve when grown in a test tube ({Link]a). Its 
growth levels off as the population depletes the nutrients that are necessary 
for its growth. In the real world, however, there are variations to this 
idealized curve. Examples in wild populations include sheep and harbor 
seals ({link]b). In both examples, the population size exceeds the carrying 
capacity for short periods of time and then falls below the carrying capacity 
afterwards. This fluctuation in population size continues to occur as the 
population oscillates around its carrying capacity. Still, even with this 
oscillation, the logistic model is confirmed. 


Note: 
Art Connection 


Number of seals 


1975 1980 1985 1990 1995 2000 
Year 


(b) 


(a) Yeast grown in ideal conditions in a test tube 
shows a Classical S-shaped logistic growth curve, 
whereas (b) a natural population of seals shows real- 
world fluctuation. The yeast is visualized using 
differential interference contrast light micrography. 
(credit a: scale-bar data from Matt Russell) 


If the major food source of seals declines due to pollution or overfishing, 
which of the following would likely occur? 


a. The carrying capacity of seals would decrease, as would the seal 
population. 


b. The carrying capacity of seals would decrease, but the seal population 
would remain the same. 

c. The number of seal deaths would increase, but the number of births 
would also increase, so the population size would remain the same. 

d. The carrying capacity of seals would remain the same, but the 
population of seals would decrease. 


Population Dynamics and Regulation 


The logistic model of population growth, while valid in many natural 
populations and a useful model, is a simplification of real-world population 
dynamics. Implicit in the model is that the carrying capacity of the 
environment does not change, which is not the case. The carrying capacity 
varies annually. For example, some summers are hot and dry whereas others 
are cold and wet; in many areas, the carrying capacity during the winter is 
much lower than it is during the summer. Also, natural events such as 
earthquakes, volcanoes, and fires can alter an environment and hence its 
carrying capacity. Additionally, populations do not usually exist in isolation. 
They share the environment with other species, competing with them for 
the same resources (interspecific competition). These factors are also 
important to understanding how a specific population will grow. 


Population growth is regulated in a variety of ways. These are grouped into 
density-dependent factors, in which the density of the population affects 
growth rate and mortality, and density-independent factors, which cause 
mortality in a population regardless of population density. Wildlife 
biologists, in particular, want to understand both types because this helps 
them manage populations and prevent extinction or overpopulation. 


Density-dependent Regulation 


Most density-dependent factors are biological in nature and include 
predation, inter- and intraspecific competition, and parasites. Usually, the 
denser a population is, the greater its mortality rate. For example, during 


intra- and interspecific competition, the reproductive rates of the species 
will usually be lower, reducing their populations’ rate of growth. In 
addition, low prey density increases the mortality of its predator because it 
has more difficulty locating its food source. Also, when the population is 
denser, diseases spread more rapidly among the members of the population, 
which affect the mortality rate. 


Density dependent regulation was studied in a natural experiment with wild 
donkey populations on two sites in Australia.!22™°'e] On one site the 
population was reduced by a population control program; the population on 
the other site received no interference. The high-density plot was twice as 
dense as the low-density plot. From 1986 to 1987 the high-density plot saw 
no change in donkey density, while the low-density plot saw an increase in 
donkey density. The difference in the growth rates of the two populations 
was caused by mortality, not by a difference in birth rates. The researchers 
found that numbers of offspring birthed by each mother was unaffected by 
density. Growth rates in the two populations were different mostly because 
of juvenile mortality caused by the mother’s malnutrition due to scarce 
high-quality food in the dense population. [link] shows the difference in 
age-specific mortalities in the two populations. 

David Choquenot, “Density-Dependent Growth, Body Condition, and 
Demography in Feral Donkeys: Testing the Food Hypothesis,” Ecology 72, 
no. 3 (June 1991):805-813. 


0.7 


® High-density population 
® Low-density population 


Mortality rate 


0.5 2.5 4.5 6.5 8.5 210.5 
Age (years) 


This graph shows the age-specific 


mortality rates for wild donkeys 
from high- and low-density 
populations. The juvenile 
mortality is much higher in the 
high-density population because 
of maternal malnutrition caused by 
a shortage of high-quality food. 


Density-independent Regulation and Interaction with Density- 
dependent Factors 


Many factors that are typically physical in nature cause mortality of a 
population regardless of its density. These factors include weather, natural 
disasters, and pollution. An individual deer will be killed in a forest fire 
regardless of how many deer happen to be in that area. Its chances of 
survival are the same whether the population density is high or low. The 
same holds true for cold winter weather. 


In real-life situations, population regulation is very complicated and 
density-dependent and independent factors can interact. A dense population 
that suffers mortality from a density-independent cause will be able to 
recover differently than a sparse population. For example, a population of 
deer affected by a harsh winter will recover faster if there are more deer 
remaining to reproduce. 


Demographic-Based Population Models 


Population ecologists have hypothesized that suites of characteristics may 
evolve in species that lead to particular adaptations to their environments. 
These adaptations impact the kind of population growth their species 
experience. Life history characteristics such as birth rates, age at first 
reproduction, the numbers of offspring, and even death rates evolve just like 
anatomy or behavior, leading to adaptations that affect population growth. 
Population ecologists have described a continuum of life-history 


“strategies” with K-selected species on one end and r-selected species on 
the other. K-selected species are adapted to stable, predictable 
environments. Populations of K-selected species tend to exist close to their 
carrying capacity. These species tend to have larger, but fewer, offspring 
and contribute large amounts of resources to each offspring. Elephants 
would be an example of a K-selected species. r-selected species are adapted 
to unstable and unpredictable environments. They have large numbers of 
small offspring. Animals that are r-selected do not provide a lot of 
resources or parental care to offspring, and the offspring are relatively self- 
sufficient at birth. Examples of r-selected species are marine invertebrates 
such as jellyfish and plants such as the dandelion. The two extreme 
strategies are at two ends of a continuum on which real species life histories 
will exist. In addition, life history strategies do not need to evolve as suites, 
but can evolve independently of each other, so each species may have some 
characteristics that trend toward one extreme or the other. 


Section Summary 


Populations with unlimited resources grow exponentially—with an 
accelerating growth rate. When resources become limiting, populations 
follow a logistic growth curve in which population size will level off at the 
Carrying capacity. 


Populations are regulated by a variety of density-dependent and density- 
independent factors. Life-history characteristics, such as age at first 
reproduction or numbers of offspring, are characteristics that evolve in 
populations just as anatomy or behavior can evolve over time. The model of 
r- and K-selection suggests that characters, and possibly suites of 
characters, may evolve adaptations to population stability near the carrying 
capacity (K-selection) or rapid population growth and collapse (r-selection). 
Species will exhibit adaptations somewhere on a continuum between these 
two extremes. 


Glossary 


birth rate 
the number of births within a population at a specific point in time 


Carrying capacity 
the maximum number of individuals of a population that can be 
supported by the limited resources of a habitat 


death rate 
the number of deaths within a population at a specific point in time 


density-dependent regulation 
the regulation of population in which birth and death rates are 
dependent on population size 


density-independent regulation 
the regulation of population in which the death rate is independent of 
the population size 


exponential growth 
an accelerating growth pattern seen in populations where resources are 
not limiting 


intraspecific competition 
the competition among members of the same species 


J-shaped growth curve 
the shape of an exponential growth curve 


K-selected species 
a species suited to stable environments that produce a few, relatively 
large offspring and provide parental care 


logistic growth 
the leveling off of exponential growth due to limiting resources 


r-selected species 
a species suited to changing environments that produce many offspring 
and provide little or no parental care 


S-shaped growth curve 
the shape of a logistic growth curve 


zero population growth 
the steady population size where birth rates and death rates are equal 


The Process of Science EnBio 
By the end of this section, you will be able to: 


Identify the shared characteristics of the natural sciences 
e Understand the process of scientific inquiry 

¢ Compare inductive reasoning with deductive reasoning 
e Describe the goals of basic science and applied science 


Formerly called blue-green algae, the (a) cyanobacteria 
seen through a light microscope are some of Earth’s 
oldest life forms. These (b) stromatolites along the 
shores of Lake Thetis in Western Australia are ancient 
structures formed by the layering of cyanobacteria in 
shallow waters. (credit a: modification of work by 
NASA; scale-bar data from Matt Russell; credit b: 
modification of work by Ruth Ellison) 


Like geology, physics, and chemistry, biology is a science that gathers 
knowledge about the natural world. Specifically, biology is the study of life. 
The discoveries of biology are made by a community of researchers who 
work individually and together using agreed-on methods. In this sense, 
biology, like all sciences is a social enterprise like politics or the arts. The 
methods of science include careful observation, record keeping, logical and 
mathematical reasoning, experimentation, and submitting conclusions to the 
scrutiny of others. Science also requires considerable imagination and 


creativity; a well-designed experiment is commonly described as elegant, or 
beautiful. Like politics, science has considerable practical implications and 
some science is dedicated to practical applications, such as the prevention 
of disease (see [link]). Other science proceeds largely motivated by 
curiosity. Whatever its goal, there is no doubt that science, including 
biology, has transformed human existence and will continue to do so. 


Biologists may choose to study Escherichia 
coli (E. coli), a bacterium that is a normal 
resident of our digestive tracts but which is 
also sometimes responsible for disease 
outbreaks. In this micrograph, the bacterium 
is visualized using a scanning electron 
microscope and digital colorization. (credit: 
Eric Erbe; digital colorization by 
Christopher Pooley, USDA-ARS) 


The Nature of Science 


Biology is a science, but what exactly is science? What does the study of 
biology share with other scientific disciplines? Science (from the Latin 


scientia, meaning "knowledge") can be defined as knowledge about the 
natural world. 


Science is a very specific way of learning, or knowing, about the world. 
The history of the past 500 years demonstrates that science is a very 
powerful way of knowing about the world; it is largely responsible for the 
technological revolutions that have taken place during this time. There are 
however, areas of knowledge and human experience that the methods of 
science cannot be applied to. These include such things as answering purely 
moral questions, aesthetic questions, or what can be generally categorized 
as spiritual questions. Science has cannot investigate these areas because 
they are outside the realm of material phenomena, the phenomena of matter 
and energy, and cannot be observed and measured. 


The scientific method is a method of research with defined steps that 
include experiments and careful observation. The steps of the scientific 
method will be examined in detail later, but one of the most important 
aspects of this method is the testing of hypotheses. A hypothesis is a 
suggested explanation for an event, which can be tested. Hypotheses, or 
tentative explanations, are generally produced within the context of a 
scientific theory. A scientific theory is a generally accepted, thoroughly 
tested and confirmed explanation for a set of observations or phenomena. 
Scientific theory is the foundation of scientific knowledge. In addition, in 
many scientific disciplines (less so in biology) there are scientific laws, 
often expressed in mathematical formulas, which describe how elements of 
nature will behave under certain specific conditions. There is not an 
evolution of hypotheses through theories to laws as if they represented 
some increase in certainty about the world. Hypotheses are the day-to-day 
material that scientists work with and they are developed within the context 
of theories. Laws are concise descriptions of parts of the world that are 
amenable to formulaic or mathematical description. 


Natural Sciences 


Some fields of science include 
astronomy, biology, computer 
science, geology, logic, physics, 
chemistry, and mathematics. 
(credit: "Image Editor"/Flickr) 


There is no complete agreement when it comes to defining what the natural 
sciences include. For some experts, the natural sciences are astronomy, 
biology, chemistry, earth science, and physics. Other scholars choose to 
divide natural sciences into life sciences, which study living things and 
include biology, and physical sciences, which study nonliving matter and 
include astronomy, physics, and chemistry. Some disciplines such as 
biophysics and biochemistry build on two sciences and are interdisciplinary. 


Scientific Inquiry 


One thing is common to all forms of science: an ultimate goal “to know.” 
Curiosity and inquiry are the driving forces for the development of science. 


Scientists seek to understand the world and the way it operates. Two 
methods of logical thinking are used: inductive reasoning and deductive 
reasoning. 


Inductive reasoning is a form of logical thinking that uses related 
observations to arrive at a general conclusion. This type of reasoning is 
common in descriptive science. A life scientist such as a biologist makes 
observations and records them. These data can be qualitative (descriptive) 
or quantitative (consisting of numbers), and the raw data can be 
supplemented with drawings, pictures, photos, or videos. From many 
observations, the scientist can infer conclusions (inductions) based on 
evidence. Inductive reasoning involves formulating generalizations inferred 
from careful observation and the analysis of a large amount of data. Brain 
studies often work this way. Many brains are observed while people are 
doing a task. The part of the brain that lights up, indicating activity, is then 
demonstrated to be the part controlling the response to that task. 


Deductive reasoning or deduction is the type of logic used in hypothesis- 
based science. In deductive reasoning, the pattern of thinking moves in the 
opposite direction as compared to inductive reasoning. Deductive 
reasoning is a form of logical thinking that uses a general principle or law 
to forecast specific results. From those general principles, a scientist can 
extrapolate and predict the specific results that would be valid as long as the 
general principles are valid. For example, a prediction would be that if the 
climate is becoming warmer in a region, the distribution of plants and 
animals should change. Comparisons have been made between distributions 
in the past and the present, and the many changes that have been found are 
consistent with a warming climate. Finding the change in distribution is 
evidence that the climate change conclusion is a valid one. 


Both types of logical thinking are related to the two main pathways of 
scientific study: descriptive science and hypothesis-based science. 
Descriptive (or discovery) science aims to observe, explore, and discover, 
while hypothesis-based science begins with a specific question or problem 
and a potential answer or solution that can be tested. The boundary between 
these two forms of study is often blurred, because most scientific endeavors 
combine both approaches. Observations lead to questions, questions lead to 


forming a hypothesis as a possible answer to those questions, and then the 
hypothesis is tested. Thus, descriptive science and hypothesis-based science 
are in continuous dialogue. 


Hypothesis Testing 


Biologists study the living world by posing questions about it and seeking 
science-based responses. This approach is common to other sciences as well 
and is often referred to as the scientific method. The scientific method was 
used even in ancient times, but it was first documented by England’s Sir 
Francis Bacon (1561-1626) ([link]), who set up inductive methods for 
scientific inquiry. The scientific method is not exclusively used by 
biologists but can be applied to almost anything as a logical problem- 
solving method. 


Sir Francis Bacon 
is credited with 
being the first to 
document the 
scientific method. 


The scientific process typically starts with an observation (often a problem 
to be solved) that leads to a question. Let’s think about a simple problem 
that starts with an observation and apply the scientific method to solve the 
problem. One Monday morning, a student arrives at class and quickly 
discovers that the classroom is too warm. That is an observation that also 
describes a problem: the classroom is too warm. The student then asks a 
question: “Why is the classroom so warm?” 


Recall that a hypothesis is a suggested explanation that can be tested. To 
solve a problem, several hypotheses may be proposed. For example, one 
hypothesis might be, “The classroom is warm because no one turned on the 
air conditioning.” But there could be other responses to the question, and 
therefore other hypotheses may be proposed. A second hypothesis might be, 
“The classroom is warm because there is a power failure, and so the air 
conditioning doesn’t work.” 


Once a hypothesis has been selected, a prediction may be made. A 
prediction is similar to a hypothesis but it typically has the format “If... 
then... .” For example, the prediction for the first hypothesis might be, “If 
the student turns on the air conditioning, then the classroom will no longer 
be too warm.” 


A hypothesis must be testable to ensure that it is valid. For example, a 
hypothesis that depends on what a bear thinks is not testable, because it can 
never be known what a bear thinks. It should also be falsifiable, meaning 
that it can be disproven by experimental results. An example of an 
unfalsifiable hypothesis is “Botticelli’s Birth of Venus is beautiful.” There is 
no experiment that might show this statement to be false. To test a 
hypothesis, a researcher will conduct one or more experiments designed to 
eliminate one or more of the hypotheses. This is important. A hypothesis 
can be disproven, or eliminated, but it can never be proven. Science does 
not deal in proofs like mathematics. If an experiment fails to disprove a 
hypothesis, then we find support for that explanation, but this is not to say 
that down the road a better explanation will not be found, or a more 
carefully designed experiment will be found to falsify the hypothesis. 


Each experiment will have one or more variables and one or more controls. 
A variable is any part of the experiment that can vary or change during the 
experiment. A control is a part of the experiment that does not change. 
Look for the variables and controls in the example that follows. As a simple 
example, an experiment might be conducted to test the hypothesis that 
phosphate limits the growth of algae in freshwater ponds. A series of 
artificial ponds are filled with water and half of them are treated by adding 
phosphate each week, while the other half are treated by adding a salt that is 
known not to be used by algae. The variable here is the phosphate (or lack 
of phosphate), the experimental or treatment cases are the ponds with added 
phosphate and the control ponds are those with something inert added, such 
as the salt. Just adding something is also a control against the possibility 
that adding extra matter to the pond has an effect. If the treated ponds show 
lesser growth of algae, then we have found support for our hypothesis. If 
they do not, then we reject our hypothesis. Be aware that rejecting one 
hypothesis does not determine whether or not the other hypotheses can be 
accepted; it simply eliminates one hypothesis that is not valid ([link]). 
Using the scientific method, the hypotheses that are inconsistent with 
experimental data are rejected. 


Note: 
Art Connection 


Make an observation 
Ask a question 


Form a hypothesis that 
answers the question 


Make a prediction based 
on the hypothesis 


Do an experiment 


to test the prediction 


Analyze the results 


Hypothesis is 
SUPPORTED 


Report results 


The scientific method is a series 
of defined steps that include 
experiments and careful 
observation. If a hypothesis is 
not supported by data, a new 
hypothesis can be proposed. 


Hypothesis is 
NOT SUPPORTED 


In the example below, the scientific method is used to solve an everyday 
problem. Which part in the example below is the hypothesis? Which is the 
prediction? Based on the results of the experiment, is the hypothesis 
supported? If it is not supported, propose some alternative hypotheses. 


1. My toaster doesn’t toast my bread. 
2. Why doesn’t my toaster work? 


3. There is something wrong with the electrical outlet. 

4. If something is wrong with the outlet, my coffeemaker also won’t 
work when plugged into it. 

5. I plug my coffeemaker into the outlet. 

6. My coffeemaker works. 


In practice, the scientific method is not as rigid and structured as it might at 
first appear. Sometimes an experiment leads to conclusions that favor a 
change in approach; often, an experiment brings entirely new scientific 
questions to the puzzle. Many times, science does not operate in a linear 
fashion; instead, scientists continually draw inferences and make 
generalizations, finding patterns as their research proceeds. Scientific 
reasoning is more complex than the scientific method alone suggests. 


Basic and Applied Science 


The scientific community has been debating for the last few decades about 
the value of different types of science. Is it valuable to pursue science for 
the sake of simply gaining knowledge, or does scientific knowledge only 
have worth if we can apply it to solving a specific problem or bettering our 
lives? This question focuses on the differences between two types of 
science: basic science and applied science. 


Basic science or “pure” science seeks to expand knowledge regardless of 
the short-term application of that knowledge. It is not focused on 
developing a product or a service of immediate public or commercial value. 
The immediate goal of basic science is knowledge for knowledge’s sake, 
though this does not mean that in the end it may not result in an application. 


In contrast, applied science or “technology,” aims to use science to solve 
real-world problems, making it possible, for example, to improve a crop 
yield, find a cure for a particular disease, or save animals threatened by a 
natural disaster. In applied science, the problem is usually defined for the 
researcher. 


Some individuals may perceive applied science as “useful” and basic 
science as “useless.” A question these people might pose to a scientist 
advocating knowledge acquisition would be, “What for?” A careful look at 
the history of science, however, reveals that basic knowledge has resulted in 
many remarkable applications of great value. Many scientists think that a 
basic understanding of science is necessary before an application is 
developed; therefore, applied science relies on the results generated through 
basic science. Other scientists think that it is time to move on from basic 
science and instead to find solutions to actual problems. Both approaches 
are valid. It is true that there are problems that demand immediate attention; 
however, few solutions would be found without the help of the knowledge 
generated through basic science. 


One example of how basic and applied science can work together to solve 
practical problems occurred after the discovery of DNA structure led to an 
understanding of the molecular mechanisms governing DNA replication. 
Strands of DNA, unique in every human, are found in our cells, where they 
provide the instructions necessary for life. During DNA replication, new 
copies of DNA are made, shortly before a cell divides to form new cells. 
Understanding the mechanisms of DNA replication enabled scientists to 
develop laboratory techniques that are now used to identify genetic 
diseases, pinpoint individuals who were at a crime scene, and determine 
paternity. Without basic science, it is unlikely that applied science would 
exist. 


Another example of the link between basic and applied research is the 
Human Genome Project, a study in which each human chromosome was 
analyzed and mapped to determine the precise sequence of DNA subunits 
and the exact location of each gene. (The gene is the basic unit of heredity; 
an individual’s complete collection of genes is his or her genome.) Other 
organisms have also been studied as part of this project to gain a better 
understanding of human chromosomes. The Human Genome Project 
({link]) relied on basic research carried out with non-human organisms and, 
later, with the human genome. An important end goal eventually became 
using the data for applied research seeking cures for genetically related 
diseases. 


The Human Genome 


Project was a 13-year 
collaborative effort 
among researchers 
working in several 

different fields of science. 
The project was 
completed in 2003. 
(credit: the U.S. 

Department of Energy 

Genome Programs) 


While research efforts in both basic science and applied science are usually 
carefully planned, it is important to note that some discoveries are made by 
serendipity, that is, by means of a fortunate accident or a lucky surprise. 
Penicillin was discovered when biologist Alexander Fleming accidentally 
left a petri dish of Staphylococcus bacteria open. An unwanted mold grew, 
killing the bacteria. The mold turned out to be Penicillium, and a new 
antibiotic was discovered. Even in the highly organized world of science, 
luck—when combined with an observant, curious mind—can lead to 
unexpected breakthroughs. 


Reporting Scientific Work 


Whether scientific research is basic science or applied science, scientists 
must share their findings for other researchers to expand and build upon 
their discoveries. Communication and collaboration within and between sub 
disciplines of science are key to the advancement of knowledge in science. 
For this reason, an important aspect of a scientist’s work is disseminating 
results and communicating with peers. Scientists can share results by 
presenting them at a scientific meeting or conference, but this approach can 
reach only the limited few who are present. Instead, most scientists present 
their results in peer-reviewed articles that are published in scientific 
journals. Peer-reviewed articles are scientific papers that are reviewed, 
usually anonymously by a scientist’s colleagues, or peers. These colleagues 
are qualified individuals, often experts in the same research area, who judge 
whether or not the scientist’s work is suitable for publication. The process 
of peer review helps to ensure that the research described in a scientific 
paper or grant proposal is original, significant, logical, and thorough. Grant 
proposals, which are requests for research funding, are also subject to peer 
review. Scientists publish their work so other scientists can reproduce their 
experiments under similar or different conditions to expand on the findings. 
The experimental results must be consistent with the findings of other 
scientists. 


There are many journals and the popular press that do not use a peer-review 
system. A large number of online open-access journals, journals with 
articles available without cost, are now available many of which use 
rigorous peer-review systems, but some of which do not. Results of any 
studies published in these forums without peer review are not reliable and 
should not form the basis for other scientific work. In one exception, 
journals may allow a researcher to cite a personal communication from 
another researcher about unpublished results with the cited author’s 
permission. 


Section Summary 


Biology is the science that studies living organisms and their interactions 
with one another and their environments. Science attempts to describe and 
understand the nature of the universe in whole or in part. Science has many 


fields; those fields related to the physical world and its phenomena are 
considered natural sciences. 


A hypothesis is a tentative explanation for an observation. A scientific 
theory is a well-tested and consistently verified explanation for a set of 
observations or phenomena. A scientific law is a description, often in the 
form of a mathematical formula, of the behavior of an aspect of nature 
under certain circumstances. Two types of logical reasoning are used in 
science. Inductive reasoning uses results to produce general scientific 
principles. Deductive reasoning is a form of logical thinking that predicts 
results by applying general principles. The common thread throughout 
scientific research is the use of the scientific method. Scientists present their 
results in peer-reviewed scientific papers published in scientific journals. 


Science can be basic or applied. The main goal of basic science is to expand 
knowledge without any expectation of short-term practical application of 
that knowledge. The primary goal of applied research, however, is to solve 
practical problems. 


Glossary 


applied science 
a form of science that solves real-world problems 


basic science 
science that seeks to expand knowledge regardless of the short-term 
application of that knowledge 


control 
a part of an experiment that does not change during the experiment 


deductive reasoning 
a form of logical thinking that uses a general statement to forecast 
specific results 


descriptive science 
a form of science that aims to observe, explore, and find things out 


falsifiable 
able to be disproven by experimental results 


hypothesis 
a suggested explanation for an event, which can be tested 


hypothesis-based science 
a form of science that begins with a specific explanation that is then 
tested 


inductive reasoning 
a form of logical thinking that uses related observations to arrive at a 
general conclusion 


life science 
a field of science, such as biology, that studies living things 


natural science 
a field of science that studies the physical world, its phenomena, and 
processes 


peer-reviewed article 
a scientific report that is reviewed by a scientist’s colleagues before 
publication 


physical science 
a field of science, such as astronomy, physics, and chemistry, that 
studies nonliving matter 


science 
knowledge that covers general truths or the operation of general laws, 
especially when acquired and tested by the scientific method 


scientific law 
a description, often in the form of a mathematical formula, for the 
behavior of some aspect of nature under certain specific conditions 


scientific method 


a method of research with defined steps that include experiments and 
careful observation 


scientific theory 
a thoroughly tested and confirmed explanation for observations or 
phenomena 


variable 
a part of an experiment that can vary or change 


Prokaryotic Cell Division EnBio 
By the end of this section, you will be able to: 


e Describe the process of binary fission in prokaryotes 


Prokaryotes such as bacteria propagate by binary fission. For unicellular 
organisms, cell division is the only method to produce new individuals. In 
both prokaryotic and eukaryotic cells, the outcome of cell reproduction is a 
pair of daughter cells that are genetically identical to the parent cell. In 
unicellular organisms, daughter cells are individuals. 


Binary Fission 


The cell division process of prokaryotes, called binary fission, is a less 
complicated and much quicker process than cell division in eukaryotes. 
Because of the speed of bacterial cell division, populations of bacteria can 
grow very rapidly. 


Section Summary 


In both prokaryotic and eukaryotic cell division, the genomic DNA is 
replicated and each copy is allocated into a daughter cell. The cytoplasmic 
contents are also divided evenly to the new cells. However, there are many 
differences between prokaryotic and eukaryotic cell division. 


Glossary 


binary fission 
the process of prokaryotic cell division 


FtsZ 
a tubulin-like protein component of the prokaryotic cytoskeleton that is 
important in prokaryotic cytokinesis (name origin: Filamenting 
temperature-sensitive mutant Z) 


origin 
the region of the prokaryotic chromosome at which replication begins 


septum 
a wall formed between bacterial daughter cells as a precursor to cell 
separation 


Sexual Reproduction EnBio 
By the end of this section, you will be able to: 


e Explain that variation among offspring is a potential evolutionary 
advantage resulting from sexual reproduction 


Sexual reproduction was an early evolutionary innovation after the 
appearance of eukaryotic cells. The fact that most eukaryotes reproduce 
sexually is evidence of its evolutionary success. In many animals, it is the 
only mode of reproduction. And yet, scientists recognize some real 
disadvantages to sexual reproduction. On the surface, offspring that are 
genetically identical to the parent may appear to be more advantageous. If 
the parent organism is successfully occupying a habitat, offspring with the 
same traits would be similarly successful. There is also the obvious benefit 
to an organism that can produce offspring by asexual budding, 
fragmentation, or asexual eggs. These methods of reproduction do not 
require another organism of the opposite sex. There is no need to expend 
energy finding or attracting a mate. That energy can be spent on producing 
more offspring. Indeed, some organisms that lead a solitary lifestyle have 
retained the ability to reproduce asexually. In addition, asexual populations 
only have female individuals, so every individual is capable of 
reproduction. In contrast, the males in sexual populations (half the 
population) are not producing offspring themselves. Because of this, an 
asexual population can grow twice as fast as a sexual population in theory. 
This means that in competition, the asexual population would have the 
advantage. All of these advantages to asexual reproduction, which are also 
disadvantages to sexual reproduction, should mean that the number of 
species with asexual reproduction should be more common. 


However, multicellular organisms that exclusively depend on asexual 
reproduction are exceedingly rare. Why is sexual reproduction so common? 
This is one of the important questions in biology and has been the focus of 
much research from the latter half of the twentieth century until now. A 
likely explanation is that the variation that sexual reproduction creates 
among offspring is very important to the survival and reproduction of those 
offspring. The only source of variation in asexual organisms is mutation. 
This is the ultimate source of variation in sexual organisms. In addition, 


those different mutations are continually reshuffled from one generation to 
the next when different parents combine their unique genomes, and the 
genes are mixed into different combinations by the process of meiosis. 
Meiosis is the division of the contents of the nucleus that divides the 
chromosomes among gametes. Variation is introduced during meiosis, as 
well as when the gametes combine in fertilization. 


Section Summary 


Nearly all eukaryotes undergo sexual reproduction. The variation 
introduced into the reproductive cells by meiosis appears to be one of the 
advantages of sexual reproduction that has made it so successful. Meiosis 
and fertilization alternate in sexual life cycles. The process of meiosis 
produces genetically unique reproductive cells called gametes, which have 
half the number of chromosomes as the parent cell. Fertilization, the fusion 
of haploid gametes from two individuals, restores the diploid condition. 
Thus, sexually reproducing organisms alternate between haploid and 
diploid stages. However, the ways in which reproductive cells are produced 
and the timing between meiosis and fertilization vary greatly. demonstrated 
by plants and some algae. 


Glossary 


alternation of generations 
a life-cycle type in which the diploid and haploid stages alternate 


diploid-dominant 
a life-cycle type in which the multicellular diploid stage is prevalent 


haploid-dominant 
a life-cycle type in which the multicellular haploid stage is prevalent 


gametophyte 
a multicellular haploid life-cycle stage that produces gametes 


germ cell 
a specialized cell that produces gametes, such as eggs or sperm 


life cycle 
the sequence of events in the development of an organism and the 
production of cells that produce offspring 


meiosis 
a nuclear division process that results in four haploid cells 


sporophyte 
a multicellular diploid life-cycle stage that produces spores 


The Structure of DNA EnBio 
By the end of this section, you will be able to: 


¢ Describe the structure of DNA 
e Describe how eukaryotic and prokaryotic DNA is arranged in the cell 


In the 1950s, Francis Crick and James Watson worked together at the 
University of Cambridge, England, to determine the structure of DNA. X- 
ray crystallography is a method for investigating molecular structure 
Researcher Rosalind Franklin used X-ray crystallography to understand the 
structure of DNA. Watson and Crick were able to piece together the puzzle 
of the DNA molecule using Franklin's data ([link]). 


(a) (b) 


Pioneering scientists (a) James Watson and Francis Crick 
are pictured here with American geneticist Maclyn 
McCarty. Scientist Rosalind Franklin discovered (b) the 
X-ray diffraction pattern of DNA, which helped to 
elucidate its double helix structure. (credit a: 
modification of work by Marjorie McCarty; b: 
modification of work by NIH) 


Now let’s consider the structure of the two types of nucleic acids, 
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The building 
blocks of DNA are nucleotides, which are made up of three parts: a 
deoxyribose (5-carbon sugar), a phosphate group, and a nitrogenous base 


({link]). There are four types of nitrogenous bases in DNA. Adenine (A) 
and guanine (G) are double-ringed purines, and cytosine (C) and thymine 
(T) are smaller, single-ringed pyrimidines. The nucleotide is named 
according to the nitrogenous base it contains. 


Pyrimidines 


Thymine 
T 


Purines 


NH> 
| 


acti 
Woe aH 
H 


Guanine Adenine 
G A 


(a) Each DNA nucleotide is made up of a sugar, a 
phosphate group, and a base. (b) Cytosine and thymine 
are pyrimidines. Guanine and adenine are purines. 


The phosphate group of one nucleotide bonds covalently with the sugar 
molecule of the next nucleotide, and so on, forming a long polymer of 
nucleotide monomers. The sugar—phosphate groups line up in a “backbone” 
for each single strand of DNA, and the nucleotide bases stick out from this 
backbone. The phosphate group is attached to the 5' carbon of one 
nucleotide and the 3' carbon of the next nucleotide. In its natural state, each 
DNA molecule is actually composed of two single strands held together 
along their length with hydrogen bonds between the bases. 


Watson and Crick proposed that the DNA is made up of two strands that are 
twisted around each other to form a right-handed helix, called a double 
helix. Base-pairing takes place between a purine and pyrimidine: namely, A 
pairs with T, and G pairs with C. In other words, adenine and thymine are 
complementary base pairs, and cytosine and guanine are also 
complementary base pairs. Because of their complementarity, there is as 
much adenine as thymine ina DNA molecule and as much guanine as 


cytosine. Adenine and thymine are connected by two hydrogen bonds, and 


cytosine and guanine are connected by three hydrogen bonds. ((link]). 
Hydrogen bonds 
Adenine 


Nitrogenous bases: , Thymine _--H2N N 3' 

3" 5!  @==PAdenine e p ‘ OH 
[== Thymine 05,0 _-+-N \ aw 
—EEPGuanine -F O N \sy 0” ‘Yo 
[==x Cytosine C Ps 


‘i a 

O,_O N o- 

ee om ys § 

Base pair S) oO. LN NH = 0520 
a weer 0 Cytosine 9, 

Sugar © Guanine 2 © 


phosphate 
backbone 


Sugar-phosphate Bases Sugar-phosphate 
3 5’ backbone backbone 


(a) (b) 


DNA (a) forms a double stranded helix, and (b) 
adenine pairs with thymine and cytosine pairs with 
guanine. (credit a: modification of work by Jerome 

Walker, Dennis Myts) 


The Structure of RNA 


There is a second nucleic acid in all cells called ribonucleic acid, or RNA. 
Like DNA, RNA is a polymer of nucleotides. Each of the nucleotides in 
RNA is made up of a nitrogenous base, a five-carbon sugar, and a 
phosphate group. In the case of RNA, the five-carbon sugar is ribose, not 
deoxyribose. ([link]). 


OH H 
Ribose Deoxyribose 


The difference between the ribose 
found in RNA and the deoxyribose 
found in DNA is that ribose has a 
hydroxyl group at the 2' carbon. 


RNA nucleotides contain the nitrogenous bases adenine, cytosine, and 
guanine. However, they do not contain thymine, which is instead replaced 
by uracil, symbolized by a “U.” RNA exists as a single-stranded molecule 
rather than a double-stranded helix. Molecular biologists have named 
several kinds of RNA on the basis of their function. These include 
messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA 
(rRNA)—molecules that are involved in the production of proteins from the 
DNA code. 


How DNA Is Arranged in the Cell 


DNA is a working molecule; it must be replicated when a cell is ready to 
divide, and it must be “read” to produce the molecules, such as proteins, to 
carry out the functions of the cell. For this reason, the DNA is protected and 
packaged in very specific ways. In addition, DNA molecules can be very 
long. Stretched end-to-end, the DNA molecules in a single human cell 
would come to a length of about 2 meters. Thus, the DNA for a cell must be 
packaged in a very ordered way to fit and function within a structure (the 
cell) that is not visible to the naked eye. The chromosomes of prokaryotes 
are much simpler than those of eukaryotes in many of their features ([link]). 
Most prokaryotes contain a single, circular chromosome that is found in an 
area in the cytoplasm called the nucleoid. 


Nucleoid 
(folded 
chromosome) 


Eukaryote Prokaryote 


A eukaryote contains a well-defined nucleus, 
whereas in prokaryotes, the chromosome lies in the 
cytoplasm in an area called the nucleoid. 


The size of the genome in one of the most well-studied prokaryotes, 
Escherichia coli, is 4.6 million base pairs, which would extend a distance of 
about 1.6 mm if stretched out. So how does this fit inside a small bacterial 
cell? The DNA is twisted beyond the double helix in what is known as 
supercoiling. Some proteins are known to be involved in the supercoiling; 
other proteins and enzymes help in maintaining the supercoiled structure. 


Eukaryotes, whose chromosomes each consist of a linear DNA molecule, 
employ a different type of packing strategy to fit their DNA inside the 
nucleus ({link]). At the most basic level, DNA is wrapped around proteins 
known as histones to form structures called nucleosomes. The DNA is 
wrapped tightly around the histone core. This nucleosome is linked to the 
next one by a short strand of DNA that is free of histones. This is also 
known as the “beads on a string” structure; the nucleosomes are the “beads” 
and the short lengths of DNA between them are the “string.” The 
nucleosomes, with their DNA coiled around them, stack compactly onto 
each other to form a 30-nm—wide fiber. This fiber is further coiled into a 
thicker and more compact structure. At the metaphase stage of mitosis, 
when the chromosomes are lined up in the center of the cell, the 


chromosomes are at their most compacted. They are approximately 700 nm 
in width, and are found in association with scaffold proteins. 


In interphase, the phase of the cell cycle between mitoses at which the 
chromosomes are decondensed, eukaryotic chromosomes have two distinct 
regions that can be distinguished by staining. There is a tightly packaged 
region that stains darkly, and a less dense region. The darkly staining 
regions usually contain genes that are not active, and are found in the 
regions of the centromere and telomeres. The lightly staining regions 
usually contain genes that are active, with DNA packaged around 
nucleosomes but not further compacted. 


Organization of Eukaryotic Chromosomes 


DNA double 
helix 


DNA wrapped 
around histone 


Nucleosomes 
coiled into a 
chromatin 
fiber 


Further 
condensation 
of chromatin 


Duplicated 
chromosome 


These figures illustrate the 
compaction of the eukaryotic 


chromosome. 


Note: 
Concept in Action 


— 
mss Openstax COLLEGE 


Route E 
De) age 


Watch this animation of DNA packaging. 


Section Summary 


The model of the double-helix structure of DNA was proposed by Watson 
and Crick. The DNA molecule is a polymer of nucleotides. Each nucleotide 
is composed of a nitrogenous base, a five-carbon sugar (deoxyribose), and a 
phosphate group. There are four nitrogenous bases in DNA, two purines 
(adenine and guanine) and two pyrimidines (cytosine and thymine). A DNA 
molecule is composed of two strands. Each strand is composed of 
nucleotides bonded together covalently between the phosphate group of one 
and the deoxyribose sugar of the next. From this backbone extend the bases. 
The bases of one strand bond to the bases of the second strand with 
hydrogen bonds. Adenine always bonds with thymine, and cytosine always 
bonds with guanine. The bonding causes the two strands to spiral around 
each other in a shape called a double helix. Ribonucleic acid (RNA) is a 
second nucleic acid found in cells. RNA is a single-stranded polymer of 
nucleotides. It also differs from DNA in that it contains the sugar ribose, 
rather than deoxyribose, and the nucleotide uracil rather than thymine. 


Various RNA molecules function in the process of forming proteins from 
the genetic code in DNA. 


Prokaryotes contain a single, double-stranded circular chromosome. 
Eukaryotes contain double-stranded linear DNA molecules packaged into 
chromosomes. The DNA helix is wrapped around proteins to form 
nucleosomes. The protein coils are further coiled, and during mitosis and 
meiosis, the chromosomes become even more greatly coiled to facilitate 
their movement. Chromosomes have two distinct regions which can be 
distinguished by staining, reflecting different degrees of packaging and 
determined by whether the DNA in a region is being expressed 
(euchromatin) or not (heterochromatin). 


Multiple Choice 


Exercise: 


Problem: Which of the following does cytosine pair with? 


a. guanine 
b. thymine 
c. adenine 
d. a pyrimidine 


Solution: 


A 
Exercise: 


Problem: 


Prokaryotes contain a chromosome, and eukaryotes contain 
chromosomes. 


a. single-stranded circular; single-stranded linear 
b. single-stranded linear; single-stranded circular 


c. double-stranded circular; double-stranded linear 
d. double-stranded linear; double-stranded circular 


Solution: 


C 


Free Response 


Exercise: 


Problem: Describe the organization of the eukaryotic chromosome. 
Solution: 


The DNA is wound around proteins called histones. The histones then 
stack together in a compact form that creates a fiber that is 30-nm 
thick. The fiber is further coiled for greater compactness. During 
metaphase of mitosis, the chromosome is at its most compact to 
facilitate chromosome movement. During interphase, there are denser 
areas of chromatin, called heterochromatin, that contain DNA that is 
not expressed, and less dense euchromatin that contains DNA that is 
expressed. 


Exercise: 


Problem: 
Describe the structure and complementary base pairing of DNA. 
Solution: 


A single strand of DNA is a polymer of nucleic acids joined covalently 
between the phosphate group of one and the deoxyribose sugar of the 
next to for a “backbone” from which the nitrogenous bases stick out. 
In its natural state, DNA has two strands wound around each other in a 
double helix. The bases on each strand are bonded to each other with 


hydrogen bonds. Only specific bases bond with each other; adenine 
bonds with thymine, and cytosine bonds with guanine. 


Glossary 


deoxyribose 
a five-carbon sugar molecule with a hydrogen atom rather than a 
hydroxyl group in the 2' position; the sugar component of DNA 
nucleotides 


double helix 
the molecular shape of DNA in which two strands of nucleotides wind 
around each other in a spiral shape 


nitrogenous base 
a nitrogen-containing molecule that acts as a base; often referring to 
one of the purine or pyrimidine components of nucleic acids 


phosphate group 
a molecular group consisting of a central phosphorus atom bound to 
four oxygen atoms 


Threats to Biodiversity EnBio 
By the end of this section, you will be able to: 


e Identify significant threats to biodiversity 

e Explain the effects of habitat loss, exotic species, and hunting on 
biodiversity 

e Identify the early and predicted effects of climate change on 
biodiversity 


The core threat to biodiversity on the planet, and therefore a threat to 
human welfare, is the combination of human population growth and the 
resources used by that population. The human population requires resources 
to survive and grow, and those resources are being removed unsustainably 
from the environment. The three greatest proximate threats to biodiversity 
are habitat loss, overharvesting, and introduction of exotic species. The first 
two of these are a direct result of human population growth and resource 
use. The third results from increased mobility and trade. A fourth major 
cause of extinction, anthropogenic (human-caused) climate change, has not 
yet had a large impact, but it is predicted to become significant during this 
century. Global climate change is also a consequence of human population 
needs for energy and the use of fossil fuels to meet those needs ((link]). 
Environmental issues, such as toxic pollution, have specific targeted effects 
on species, but are not generally seen as threats at the magnitude of the 
others. 


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Years before present 


Atmospheric carbon dioxide levels fluctuate in a 
cyclical manner. However, the burning of fossil 
fuels in recent history has caused a dramatic 
increase in the levels of carbon dioxide in the 
Earth’s atmosphere, which have now reached 
levels never before seen on Earth. Scientists 
predict that the addition of this “greenhouse gas’ 
to the atmosphere is resulting in climate change 
that will significantly impact biodiversity in the 
coming century. 


9 


Overharvesting 


Overharvesting is a serious threat to many species, but particularly to 
aquatic species. There are many examples of regulated fisheries (including 
hunting of marine mammals and harvesting of crustaceans and other 
species) monitored by fisheries scientists that have nevertheless collapsed. 
The western Atlantic cod fishery is the most spectacular recent collapse. 
While it was a hugely productive fishery for 400 years, the introduction of 
modern factory trawlers in the 1980s and the pressure on the fishery led to 


it becoming unsustainable. The causes of fishery collapse are both 
economic and political in nature. Most fisheries are managed as a common 
resource, available to anyone willing to fish, even when the fishing territory 
lies within a country’s territorial waters. Common resources are subject to 
an economic pressure known as the tragedy of the commons, in which 
fishers have little motivation to exercise restraint in harvesting a fishery 
when they do not own the fishery. The general outcome of harvests of 
resources held in common is their overexploitation. While large fisheries 
are regulated to attempt to avoid this pressure, it still exists in the 
background. This overexploitation is exacerbated when access to the fishery 
is open and unregulated and when technology gives fishers the ability to 
overfish. In a few fisheries, the biological growth of the resource is less 
than the potential growth of the profits made from fishing if that time and 
money were invested elsewhere. In these cases—whales are an example— 
economic forces will drive toward fishing the population to extinction. 


Note: 
Concept in Action 


oR esas 


Explore a U.S. Fish & Wildlife Service interactive map of critical habitat 
for endangered and threatened species in the United States. To begin, select 
“Visit the online mapper.” 


For the most part, fishery extinction is not equivalent to biological 
extinction—the last fish of a species is rarely fished out of the ocean. But 
there are some instances in which true extinction is a possibility. Whales 
have slow-growing populations and are at risk of complete extinction 
through hunting. Also, there are some species of sharks with restricted 


distributions that are at risk of extinction. The groupers are another 
population of generally slow-growing fishes that, in the Caribbean, includes 
a number of species that are at risk of extinction from overfishing. 


Coral reefs are extremely diverse marine ecosystems that face peril from 
several processes. Reefs are home to 1/3 of the world’s marine fish species 
—about 4000 species—despite making up only one percent of marine 
habitat. Most home marine aquaria house coral reef species that are wild- 
caught organisms—not cultured organisms. Although no marine species is 
known to have been driven extinct by the pet trade, there are studies 
showing that populations of some species have declined in response to 
harvesting, indicating that the harvest is not sustainable at those levels. 
There are also concerns about the effect of the pet trade on some terrestrial 
species such as turtles, amphibians, birds, plants, and even the orangutans. 


Note: 
Concept in Action 


View a brief video discussing the role of marine ecosystems in supporting 
human welfare and the decline of ocean ecosystems. 


Section Summary 


The core threats to biodiversity are human population growth and 
unsustainable resource use. To date, the most significant causes of 
extinction are habitat loss, introduction of exotic species, and 
overharvesting. Climate change is predicted to be a significant cause of 
extinction in the coming century. Habitat loss occurs through deforestation, 


damming of rivers, and other activities. Overharvesting is a threat 
particularly to aquatic species, but the taking of bush meat in the humid 
tropics threatens many species in Asia, Africa, and the Americas. Exotic 
species have been the cause of a number of extinctions and are especially 
damaging to islands and lakes. Exotic species’ introductions are increasing 
because of the increased mobility of human populations and growing global 
trade and transportation. Climate change is forcing range changes that may 
lead to extinction. It is also affecting adaptations to the timing of resource 
availability that negatively affects species in seasonal environments. The 
impacts of climate change are currently greatest in the arctic. Global 
warming will also raise sea levels, eliminating some islands and reducing 
the area of all others. 


Glossary 


bush meat 
a wild-caught animal used as food (typically mammals, birds, and 
reptiles); usually referring to hunting in the tropics of sub-Saharan 
Africa, Asia, and the Americas 


chytridiomycosis 
a disease of amphibians caused by the fungus Batrachochytrium 
dendrobatidis; thought to be a major cause of the global amphibian 
decline 


exotic species 
(also, invasive species) a species that has been introduced to an 
ecosystem in which it did not evolve 


tragedy of the commons 
an economic principle that resources held in common will inevitably 
be over-exploited 


white-nose syndrome 
a disease of cave-hibernating bats in the eastern United States and 
Canada associated with the fungus Geomyces destructans 


Transcription EnBio 
By the end of this section, you will be able to: 


e Explain the central dogma 
e Explain the main steps of transcription 
e Describe how eukaryotic mRNA is processed 


In both prokaryotes and eukaryotes, the second function of DNA (the first 
was replication) is to provide the information needed to construct the 
proteins necessary so that the cell can perform all of its functions. To do 
this, the DNA is “read” or transcribed into an mRNA molecule. The mRNA 
then provides the code to form a protein by a process called translation. 
Through the processes of transcription and translation, a protein is built 
with a specific sequence of amino acids that was originally encoded in the 
DNA. This module discusses the details of transcription. 


The Central Dogma: DNA Encodes RNA; RNA Encodes 
Protein 


The flow of genetic information in cells from DNA to mRNA to protein is 
described by the central dogma ([link]), which states that genes specify the 
sequences of mRNAs, which in turn specify the sequences of proteins. 


Protein 


The central dogma states that 


DNA encodes RNA, which in turn 
encodes protein. 


The copying of DNA to mRNA is relatively straightforward, with one 
nucleotide being added to the mRNA strand for every complementary 
nucleotide read in the DNA strand. The translation to protein is more 
complex because groups of three mRNA nucleotides correspond to one 
amino acid of the protein sequence. However, as we shall see in the next 
module, the translation to protein is still systematic, such that nucleotides 1 
to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino 
acid 2, and so on. 


Transcription: from DNA to mRNA 


Transcription always proceeds from one of the two DNA strands, which is 
called the template strand. The mRNA product is complementary to the 
template strand and is almost identical to the other DNA strand, called the 
nontemplate strand, with the exception that RNA contains a uracil (U) in 
place of the thymine (T) found in DNA. During elongation, an enzyme 
called RNA polymerase proceeds along the DNA template adding 
nucleotides by base pairing with the DNA template in a manner similar to 
DNA replication, with the difference that an RNA strand is being 
synthesized that does not remain bound to the DNA template. As elongation 
proceeds, the DNA is continuously unwound ahead of the core enzyme and 
rewound behind it ([Link]). 


Nontemplate strand 


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DNA RNA polymerase Template strand 


During elongation, RNA polymerase tracks along the 
DNA template, synthesizes mRNA in the 5' to 3 
direction, and unwinds then rewinds the DNA as it is 
read. 


Section Summary 


In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the 
DNA template. Elongation synthesizes new mRNA. Termination liberates 
the mRNA and occurs by mechanisms that stall the RNA polymerase and 
cause it to fall off the DNA template. Newly transcribed eukaryotic mRNAs 
are modified with a cap and a poly-A tail. These structures protect the 
mature MRNA from degradation and help export it from the nucleus. 
Eukaryotic mRNAs also undergo splicing, in which introns are removed 
and exons are reconnected with single-nucleotide accuracy. Only finished 
mRNAs are exported from the nucleus to the cytoplasm. 


Glossary 


exon 
a sequence present in protein-coding mRNA after completion of pre- 
mRNA splicing 


intron 


non—protein-coding intervening sequences that are spliced from 
mRNA during processing 


mRNA 
messenger RNA; a form of RNA that carries the nucleotide sequence 
code for a protein sequence that is translated into a polypeptide 
sequence 


nontemplate strand 
the strand of DNA that is not used to transcribe mRNA; this strand is 
identical to the mRNA except that T nucleotides in the DNA are 
replaced by U nucleotides in the mRNA 


promoter 
a sequence on DNA to which RNA polymerase and associated factors 
bind and initiate transcription 


RNA polymerase 
an enzyme that synthesizes an RNA strand from a DNA template 
strand 


splicing 
the process of removing introns and reconnecting exons in a pre- 
mRNA 


template strand 
the strand of DNA that specifies the complementary mRNA molecule 


transcription bubble 
the region of locally unwound DNA that allows for transcription of 
mRNA 


Translation EnBio 
By the end of this section, you will be able to: 


e Describe the different steps in protein synthesis 
e Describe the genetic code and how the nucleotide sequence determines 
the amino acid and the protein sequence 


The synthesis of proteins is one of a cell’s most energy-consuming 
metabolic processes. In turn, proteins account for more mass than any other 
component of living organisms (with the exception of water), and proteins 
perform a wide variety of the functions of a cell. The process of translation, 
or protein synthesis, involves decoding an mRNA message into a 
polypeptide product. Amino acids are covalently strung together in lengths 
ranging from approximately 50 amino acids to more than 1,000. 


The Protein Synthesis Machinery 


In addition to the mRNA template, many other molecules contribute to the 
process of translation. The composition of each component may vary across 
species; for instance, ribosomes may consist of different numbers of 
ribosomal RNAs (rRNA) and polypeptides depending on the organism. 
However, the general structures and functions of the protein synthesis 
machinery are comparable from bacteria to human cells. Translation 
requires the input of an mRNA template, ribosomes, tRNAs, and various 
enzymatic factors ([link]). 


Amino acids 


Growing 


protein chain Ribosome 


tRNA 


mRNA 


The protein synthesis machinery 
includes the large and small 
subunits of the ribosome, mRNA, 
and tRNA. (credit: modification of 
work by NIGMS, NIH) 


In E. coli, there are 200,000 ribosomes present in every cell at any given 
time. A ribosome is a complex macromolecule composed of structural and 
catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the 
nucleolus is completely specialized for the synthesis and assembly of 
rRNAs. 


Ribosomes are located in the cytoplasm in prokaryotes and in the cytoplasm 
and endoplasmic reticulum of eukaryotes. Ribosomes are made up of a 
large and a small subunit that come together for translation. The small 
subunit is responsible for binding the mRNA template, whereas the large 
subunit sequentially binds tRNAs, a type of RNA molecule that brings 
amino acids to the growing chain of the polypeptide. Each mRNA molecule 
is simultaneously translated by many ribosomes, all synthesizing protein in 
the same direction. 


Depending on the species, 40 to 60 types of tRNA exist in the cytoplasm. 
Serving as adaptors, specific tRNAs bind to sequences on the mRNA 


template and add the corresponding amino acid to the polypeptide chain. 
Therefore, tRNAs are the molecules that actually “translate” the language 
of RNA into the language of proteins. For each tRNA to function, it must 
have its specific amino acid bonded to it. In the process of tRNA 
“charging,” each tRNA molecule is bonded to its correct amino acid. 


The Genetic Code 


To summarize what we know to this point, the cellular process of 
transcription generates messenger RNA (MRNA), a mobile molecular copy 
of one or more genes with an alphabet of A, C, G, and uracil (U). 
Translation of the mRNA template converts nucleotide-based genetic 
information into a protein product. Protein sequences consist of 20 
commonly occurring amino acids; therefore, it can be said that the protein 
alphabet consists of 20 letters. Each amino acid is defined by a three- 
nucleotide sequence called the triplet codon. The relationship between a 
nucleotide codon and its corresponding amino acid is called the genetic 
code. 


Given the different numbers of “letters” in the mRNA and protein 
“alphabets,” combinations of nucleotides corresponded to single amino 
acids. Using a three-nucleotide code means that there are a total of 64 (4 x 4 
x 4) possible combinations; therefore, a given amino acid is encoded by 
more than one nucleotide triplet ({link]). 


Second letter 


UAU UGU 
uact™® luec to 


UAA Stop|UGA Stop 
UAG Stop|UGG Trp 


First letter 


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Cc 
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Cc 
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This figure shows the genetic code for 
translating each nucleotide triplet, or 
codon, in mRNA into an amino acid 

or a termination signal in a nascent 
protein. (credit: modification of work 
by NIH) 


Three of the 64 codons terminate protein synthesis and release the 
polypeptide from the translation machinery. These triplets are called stop 
codons. Another codon, AUG, also has a special function. In addition to 
specifying the amino acid methionine, it also serves as the start codon to 
initiate translation. The reading frame for translation is set by the AUG start 
codon near the 5' end of the mRNA. The genetic code is universal. With a 
few exceptions, virtually all species use the same genetic code for protein 
synthesis, which is powerful evidence that all life on Earth shares a 
common origin. 


Section Summary 


The central dogma describes the flow of genetic information in the cell 
from genes to mRNA to proteins. Genes are used to make MRNA by the 


process of transcription; MRNA is used to synthesize proteins by the 
process of translation. The genetic code is the correspondence between the 
three-nucleotide mRNA codon and an amino acid. The genetic code is 
“translated” by the tRNA molecules, which associate a specific codon with 
a specific amino acid. The genetic code is degenerate because 64 triplet 
codons in mRNA specify only 20 amino acids and three stop codons. This 
means that more than one codon corresponds to an amino acid. Almost 
every species on the planet uses the same genetic code. 


Glossary 


codon 
three consecutive nucleotides in mRNA that specify the addition of a 
specific amino acid or the release of a polypeptide chain during 
translation 


genetic code 
the amino acids that correspond to three-nucleotide codons of MRNA 


rRNA 
ribosomal RNA; molecules of RNA that combine to form part of the 
ribosome 


stop codon 
one of the three mRNA codons that specifies termination of translation 


start codon 
the AUG (or, rarely GUG) on an mRNA from which translation 
begins; always specifies methionine 


tRNA 
transfer RNA; an RNA molecule that contains a specific three- 
nucleotide anticodon sequence to pair with the mRNA codon and also 
binds to a specific amino acid